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Learning Objectives
• Compare and contrast the routes of transmission for various tapeworms and describe their life cycles
Tapeworms are characterized as adult parasitic flatworms that target and infect the digestive tract. Typically, transmission occurs by ingestion of a live tapeworm larva which is found in undercooked or contaminated food. Once inside the digestive tract, the larvae can then grow and develop into a large tapeworm. There are various types of tapeworms identified to date that are capable of infecting humans. A few common tapeworms include the pork tapeworm (Taenia solium), the beef tapeworm (Taenia saginata), and the fish tapeworm (Diphyllobothrium spp. ).
Taenia solium
Taenia solium, the pork tapeworm, infects both pigs and humans. Humans are typically infected by ingesting infected pork. Taenia solium will target the intestinal area in humans. Using the four suckers and two rows of hooks present on its scolex, it lodges itself against the intestinal wall. Once anchored, the tapeworm continues to grow in the intestine and will pass its eggs through the feces. When Taenia solium is in its larval stage, it is referred to as a cysticercus and can cause cysticercosis. Cysticercosis occurs when the cysticerci reach the central nervous system and cause neurological issues.
Taenia saginata
Taenia saginata, the beef tapeworm, is capable of infecting both cattle and humans. Infection by Taenia saginata is referred to as taeniasis in humans and occurs by ingestion of contaminated meat that has been improperly handled. Taeniasis is caused by the ability of the tapeworm to lodge itself in the small intestine of the human and release fertilized eggs through the feces. The eggs can then infect cattle upon ingestion. Upon infection of the cattle, the fertilized eggs will develop into zygotes which will exit the digestive tract and enter into the circulatory system. The larval stages will then form cysts, referred to as Cysticercus bovis, within the muscular system of the cattle. Therefore, if humans ingest under prepared meat with cysts, the cysts will break open into the digestive system and develop into an adult tapeworm in the human host.
Diphyllobothrium spp.
Diphyllobothrium spp, the fish tapeworm, encompasses various species that can infect humans upon ingestion of under cooked or raw fish. For example, these tapeworms include those found on broad fish and salmon. Interestingly, only a few species of these tapeworms are found to infect humans on a frequent basis. The tapeworms found in fish exhibit the ability to also infect canines, felines, bears, and mussels.
The life cycle for fish tapeworms includes movement through numerous hosts. The mammal host is considered the definitive host as this is the site of worm reproduction. The immature eggs are passed through the feces of the mammal host and then infect a freshwater host. This freshwater host is considered to be the intermediate host. The intermediate host is then ingested by a second intermediate host which includes the fish. The larvae, which developed in the first intermediate host, then migrate out into the flesh of the fish (the second intermediate host). The larvae develop into a more mature form and constitute the infective stage for the definitive host. It is important to note that many second intermediate hosts are ingested by larger predator species that are utilized as a food source for humans. Therefore, it is not necessary for humans to directly eat the second intermediate host in order to be infected.
Key Points
• There are numerous types of tapeworms capable of infecting humans including beef, pork, and fish tapeworms.
• Taenia solium, the pork tapeworm, are passed via infected feces to the pig host but requires ingestion of under cooked pork by a human to ensure transmission.
• Taenia saginata, the beef tapeworm, are passed to humans by ingesting under cooked or raw beef that has been infected with the cyst stage in the life cycle.
• Diphyllobothrium spp, the fish tapeworm, requires multiple hosts to successfully infect a human host.
Key Terms
• scolex: The “head” of the tapeworm that contains suckers and rows of hooks by which it attaches itself to the host.
15.12B: Hydatid Disease
Learning Objectives
• Outline the life cycle of Echinococcus granulosus
Hydatid disease, commonly referred to as echinococcosis, is a result of infection by the tapeworm included in the Echinococcus spp. Echinococcus multilocularis results in alveolar echinococcosis and Echinococcus vogeli can cause polycystic echinococcosis. In individuals that develop alveolar echinococcosis, which is extremely rare, cysts develop and grow within the alveolar, liver, lungs, and brain. In the cases of alveolar echinococcosis, the parasite responsible, Echinococcus multilocularis, is associated with dogs, cats, wolves and most commonly, foxes, serving as the definitive hosts. The intermediate hosts include small rodents. In individuals that develop polycystic echinococcosis, there is the development of slow growing cysts within the body that exhibit the capability to infiltrate surrounding areas. Cysts are typically found in the liver and in the thorax or abdominal cavity. The parasite responsible for polycystic echinococcosis, Echinococcus vogeli, uses dogs or bush dogs as a definitive host and rodents as an intermediate hosts.
Echinococcus granulosus is a tapeworm found in dogs, who function as the definitive host, as well as sheep, cattle, goats, and pigs who serve as intermediate hosts. Echinococcus granulosus are capable of infecting humans, resulting in hydatid disease, and cause slowly enlarging cysts that develop in vital organs such as the liver or lungs, also referred to as cystic echinococcosis. However, the growth of these cysts are slow and may go unnoticed for a significant duration of time. This form of echinococcosis is more prevalent and commonly found in humans. The adult Echinococcus granulosus targets the small bowel of the definitive hosts and release eggs through the feces. After ingestion by the intermediate hosts, the eggs will hatch and penetrate the intestinal wall. The exiting of the intestinal wall results in circulation of oncospheres that will target various organs, including the liver and lungs. The oncospheres undergo further growth and form cysts. The definitive host will then become infected upon ingestion of the cyst-containing organs of the infected intermediate host. It is within the definitive host that the cyst will develop into the adult stage and the cycle continues and repeats.
Hydatid disease is characterized by the growth of these cysts into the adult stage for the tapeworm. Individuals infected with Echinococcus species that develop hydatid disease may not develop symptoms for many years after infection. However, if symptoms develop, it may present in the form of pain or discomfort due to the growing cysts in the upper abdominal regions. Additionally, rupture of fluid within the cysts can result in various medical issues including allergic reactions or death.
Key Points
• Echinococcus granulosus causes hydatid disease, or cystic echinococcus and causes slowly enlarging cysts to develop in vital organs.
• Echinococcus multilocularis results in alveolar echinococcosis and Echinococcus vogeli can cause polycystic echinococcosis.
• Individuals infected with Echinococcus species who develop hydatid disease may not develop symptoms for many years after infection.
Key Terms
• echinococcosis: a parasitic disease of both animals and humans, also known as hydatid disease. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.12%3A_Helminthic_Diseases_of_the_Digestive_System/15.12A%3A_Tapeworms.txt |
Learning Objectives
• Compare and contrast mechanisms of infection for the parasitic nematodes: Ascaris lumbricoides and Enterobius
Nematodes, or roundworms, are the most diverse phylum of pseudocoelomates and one of the most diverse animal phyla. Nematodes are characterized by the presence of a tubular digestive system with openings at both ends. They can be found in various ecosystems ranging from the polar regions to the tropics, fresh to marine water and various terrestrial environments ranging from mountains, deserts and oceanic floors. Nematodes are also capable of exhibiting parasitic behavior that contribute to digestive system diseases. Analysis of parasitic nematodes reveals the presence of specific body structures which promote parasitic behaviors such as ridges, rings or bristles that allow for attachment. Parasitic nematodes that commonly infect humans include ascarids (Ascaris), pinworms (Enterobius), whipworms (Trichuris trichiura), filarias and hookworms. The following is a brief overview of two of these types of roundworms, including Ascaris and Enterobious.
Ascariasis
Ascariasis is a disease that is caused by the parasitic roundworm Ascaris lumbricoides. Ascariasis is commonly found in tropical and sub-tropical regions and is transmitted by ingesting food contaminated with Ascaris eggs that are typically present in the feces of an infected individual. Upon ingestion of Ascaris eggs, the larvae continue development and hatch within the intestine of the host. The larvae burrow through the intestinal wall and begin circulation in the system and migrate to the lungs. Once they have migrated to the lungs, the larvae break into the alveoli and continue to move through the trachea and esophagus where they are eventually coughed up and swallowed. For a second time, the larvae enter into the intestine and mature into adult worms. Individuals affected with ascariasis can be asymptomatic or suffer from visceral damage due to the travel of the larvae through the body. The presence of the worms within the intestine may also result in malabsorption or intestinal blockage.
Enterobius
Enterobius, referred to as pinworm, is a type of parasitic nematode that is commonly found in the intestine of children. This infection is often called enterobiasis. The entire life cycle of the pinworm occurs within the human gastrointestinal tract. The life cycle begins with ingestion or insertion of eggs in the anus that have been transmitted via human-to-human contact. The life cycle of the Enterobious ends with eggs laid in the anus and transfered to surfaces that come in contact with this region, such as fingernails, hands, night-clothing and bed linens. Infection by pinworm is more prevalent in children due to their behaviors. Upon infection with eggs, they travel to the small intestine and hatch. The pinworm larvae will then migrate towards the colon and undergo molting which allows for further development. After two molt cycles, the larvae have developed into adults. The pinworms exhibit the ability to mate in the small intestine. Shortly after mating, the male worms die and are passed out via the feces. However, the female pinworms will attach to the mucus and wait for the egg-laying process to begin. The egg-laying process begins with the migration of the females towards the rectum. The eggs, which are covered with a sticky covering, are then released and deposited on the outside or near the anus. The cycle begins again once eggs are ingested and infect an additional host.
Key Points
• Parasitic nematodes often contain specific body structures which promote parasitic behaviors such as ridges, rings or bristles that allow for attachment.
• Two major types of roundworms that commonly infect humans include Ascaris and Enterobious.
• Ascariasis is a disease that is caused by the parasitic roundworm Ascaris lumbricoides and is transmitted by ingesting food contaminated with Ascaris eggs.
• Enterobius, referred to as pinworm, causes enterobiasis and is commonly found in the intestine of children. The entire life cycle of the pinworm occurs within the human gastrointestinal tract.
Key Terms
• visceral: of or relating to the viscera – the internal organs of the body
• nematode: A small invertebrate animal of the phylum Nematoda.
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• Helminths, Soil-Transmitted. Provided by: Centers for Disease Control and Prevention. Located at: wwwnc.cdc.gov/travel/yellowbo...intestinal.htm. License: Public Domain: No Known Copyright
• Tapeworm infection. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Tapeworm_infection. License: CC BY-SA: Attribution-ShareAlike
• Taenia saginata. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Taenia_saginata. License: CC BY-SA: Attribution-ShareAlike
• Taenia solium. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Taenia_solium. License: CC BY-SA: Attribution-ShareAlike
• Fish tapeworm. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Fish_tapeworm. License: CC BY-SA: Attribution-ShareAlike
• Parasitic worm. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Parasitic_worm. License: CC BY-SA: Attribution-ShareAlike
• Parasites: About Parasites. Provided by: Centers for Disease Control and Prevention. Located at: http://www.cdc.gov/parasites/about.html. License: Public Domain: No Known Copyright
• Taenia saginata. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Taenia_saginata. License: CC BY-SA: Attribution-ShareAlike
• scolex. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/scolex. License: CC BY-SA: Attribution-ShareAlike
• Taenia solium scolex. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ta...ium_scolex.JPG. License: Public Domain: No Known Copyright
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• Taenia saginata adult 5260 lores. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi...5260_lores.jpg. License: Public Domain: No Known Copyright
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• Parasites - Echinococcosis: Biology. Provided by: Centers for Disease Control and Prevention. Located at: http://www.cdc.gov/parasites/echinoc...s/biology.html. License: Public Domain: No Known Copyright
• Parasites - Echinococcosis. Provided by: Centers for Disease Control and Prevention. Located at: http://www.cdc.gov/parasites/echinococcosis/. License: Public Domain: No Known Copyright
• Parasites - Echinococcosis: Cystic Echinococcosis (CE) FAQs. Provided by: Centers for Disease Control and Prevention. Located at: http://www.cdc.gov/parasites/echinoc...o/ce-faqs.html. License: Public Domain: No Known Copyright
• Echinococcosis. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Echinoc...Echinococcosis. License: CC BY-SA: Attribution-ShareAlike
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• Echinococcosis. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Echinococcosis. License: CC BY-SA: Attribution-ShareAlike
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• Provided by: United States Department of Agriculture. Located at: soils.usda.gov/sqi/concepts/s...nematodes.html. License: Public Domain: No Known Copyright
• Ascarids. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ascarids. License: CC BY-SA: Attribution-ShareAlike
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The human reproductive system functions to produce human offspring, with the male providing sperm and the female providing the ovum.
Learning Objectives
• Summarize the reproductive systems of men and women
Key Points
• The male reproductive system consists of external organs. The testes in the scrotum produce the male gamete, sperm, which is ejaculated in seminal fluid by the penis.
• The female reproductive system primarily consists of internal organs. The female gamete, ovum, is produced in the ovaries and is released monthly to travel to the uterus via the Fallopian tubes.
• Fertilization can occur if the penis is inserted through the vulva into the vagina and sperm is ejaculated towards the cervix. If an ovum is currently in the uterus, it can then be fertilized by sperm that manage to enter the cervix.
• Once fertilized, an ovum becomes a zygote and if all goes well, develops into a fetus in the uterus.
• Natural birth occurs when the fetus is pushed from the vagina after nine months in the uterus.
Key Terms
• fallopian tubes: The Fallopian tubes, also known as oviducts, uterine tubes, and salpinges (singular salpinx) are two very fine tubes lined with ciliated epithelia leading from the ovaries of female mammals into the uterus, via the utero-tubal junction.
• penis: The male sexual organ for copulation and urination; the tubular portion of the male genitalia (excluding the scrotum).
• vagina: A fibromuscular tubular tract which is the female sex organ and has two main functions: sexual intercourse and childbirth.
The reproductive system or genital system is a set of organs within an organism that work together to produce offspring. Many non-living substances, such as fluids, hormones, and pheromones, are important accessories to the reproductive system. Unlike most organ systems, the sexes of differentiated species often have significant differences. These differences allow for a combination of genetic material between two individuals and thus the possibility of greater genetic fitness of the offspring.
The Reproductive Process
Human reproduction takes place as internal fertilization by sexual intercourse. During this process, the erect penis of the male is inserted into the female’s vagina until the male ejaculates semen, which contains sperm, into the vagina. The sperm travels through the vagina and cervix into the uterus for potential fertilization of an ovum. Upon successful fertilization and implantation, gestation of the fetus occurs within the female’s uterus for approximately nine months (pregnancy). Gestation ends with labor resulting in birth. In labor, the uterine muscles contract, the cervix dilates, and the baby passes out through the vagina. Human babies and children are nearly helpless and require high levels of parental care for many years. One important type of parental care is the use of the mammary glands in the female breasts to nurse the baby.
The Male Reproductive System
The human male reproductive system is a series of organs located outside of the body and around the pelvic region. The primary direct function of the male reproductive system is to provide the male gamete or spermatozoa for fertilization of the ovum. The major reproductive organs of the male can be grouped into three categories. The first category is sperm production and storage. Production takes place in the testes, housed in the temperature-regulating scrotum. Immature sperm then travel to the epididymis for development and storage. The second category, the ejaculatory fluid-producing glands, includes the seminal vesicles, prostate, and vas deferens. The final category, used for copulation and deposition of the spermatozoa (sperm) within the female, includes the penis, urethra, vas deferens, and Cowper’s gland.
Only our species has a distinctive mushroom-capped glans, which is connected to the shaft of the penis by a thin tissue of frenulum (the delicate tab of skin just beneath the urethra). One of the most significant features of the human penis is the coronal ridge underneath the gland around the circumference of the shaft. Magnetic imaging studies of heterosexual couples having sex reveal that during coitus, the typical penis expands to fill the vaginal tract, and with full penetration can even reach the woman’s cervix and lift her uterus. This combined with the fact that human ejaculate is expelled with great force and considerable distance (up to two feet if not contained), suggests that men are designed to release sperm into the uppermost portion of the vagina. This may be an evolutionary adaptation to expel the semen left by other males while at the same time increasing the possibility of fertilization with the current male’s semen.
The Female Reproductive System
The human female reproductive system is a series of organs primarily located inside the body and around the pelvic region. It contains three main parts: the vagina, which leads from the vulva, the vaginal opening, to the uterus; the uterus, which holds the developing fetus; and the ovaries, which produce the female’s ova. The breasts are also a reproductive organ during parenting, but are usually not classified as part of the female reproductive system. The vagina meets the outside at the vulva, which also includes the labia, clitoris, and urethra. During intercourse, this area is lubricated by mucus secreted by the Bartholin’s glands. The vagina is attached to the uterus through the cervix, while the uterus is attached to the ovaries via the Fallopian tubes. At certain intervals, approximately every 28 days, the ovaries release an ovum that passes through the Fallopian tube into the uterus.
If the ova is fertilized by sperm, it attaches to the endometrium and the fetus develops. In months when fertilization does not occur, the lining of the uterus, called the endometrium, and unfertilized ova are shed each cycle through a process known as menstruation. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.13%3A_Microbial_Diseases_of_the_Genitourinary_System/15.13A%3A_Overview_of_the_Male_and_Female_Reproductive_Systems.txt |
Learning Objectives
• Review the urinary system
The Renal System
The renal system, which is also called the urinary system, is a group of organs in the body that filters out excess fluid and other substances from the bloodstream. The purpose of the renal system is to eliminate wastes from the body, regulate blood volume and pressure, control levels of electrolytes and metabolites, and regulate blood pH.
The renal system organs include the kidneys, ureters, bladder, and urethra. Metabolic wastes and excess ions are filtered out of the blood, along with water, and leave the body in the form of urine.
Renal System Functions
The renal system has many functions. Many of these functions are interrelated with the physiological mechanisms in the cardiovascular and respiratory systems.
1. Removal of metabolic waste products from the body (mainly urea and uric acid).
2. Regulation of electrolyte balance (e.g., sodium, potassium, and calcium).
3. Osmoregulation controls the blood volume and body water contents.
4. Blood pressure homeostasis: The renal system alters water retention and thirst to slowly change blood volume and keep blood pressure in a normal range.
5. Regulation of acid-base homeostasis and blood pH, a function shared with the respiratory system.
Many of these functions are related to one another as well. For example, water follows ions via an osmotic gradient, so mechanisms that alter sodium levels or sodium retention in the renal system will alter water retention levels as well.
Organs of the Renal System
Kidneys and Nephrons
Kidneys are the most complex and critical part of the urinary system. The primary function of the kidneys is to maintain a stable internal environment (homeostasis) for optimal cell and tissue metabolism. The kidneys have an extensive blood supply from the renal arteries that leave the kidneys via the renal vein.
Nephrons are the main functional component inside the parenchyma of the kidneys, which filter blood to remove urea, a waste product formed by the oxidation of proteins, as well as ions like potassium and sodium. The nephrons are made up of a capsule capillaries (the glomerulus) and a small renal tube. The renal tube of the nephron consists of a network of tubules and loops that are selectively permeable to water and ions. Many hormones involved in homeostasis will alter the permeability of these tubules to change the amount of water that is retained by the body.
Ureter
Urine passes from the renal tube through tubes called ureters and into the bladder.
Bladder
The bladder is flexible and is used as storage until the urine is allowed to pass through the urethra and out of the body.
Urethra
The female and male renal system are very similar, differing only in the length of the urethra.
Human Osmoregulation
The kidneys play a very large role in human osmoregulation by regulating the amount of water reabsorbed from the glomerular filtrate in kidney tubules, which is controlled by hormones such as antidiuretic hormone (ADH), renin, aldosterone, and angiotensin I and II.
A basic example is that a decrease in water concentration of blood is detected by osmoreceptors in the hypothalamus, which stimulates ADH release from the pituitary gland to increase the permeability of the wall of the collecting ducts and tubules in the nephrons. Therefore, a large proportion of water is reabsorbed from fluid to prevent a fair proportion of water from being excreted.
The extent of blood volume and blood pressure regulation facilitated by the kidneys is a complex process. Besides ADH secretion, the renin-angiotensin feedback system is critically important to maintain blood volume and blood pressure homeostasis.
Key Points
• The renal system eliminate wastes from the body, controls levels of electrolytes and metabolites, controls the osmoregulation of blood volume and pressure, and regulates blood pH.
• The renal system organs include the kidneys, ureter, bladder, and urethra. Nephrons are the main functional component of the kidneys.
• The respiratory and cardiovascular systems have certain functions that overlap with renal system functions.
• Metabolic wastes and excess ions are filtered out of the blood, combined with water, and leave the body in the form of urine.
• A complex network of hormones controls the renal system to maintain homeostasis.
Key Terms
• ureter: These are two long, narrow ducts that carry urine from the kidneys to the urinary bladder.
• osmoregulation: The most important function of the renal system, in which blood volume, blood pressure, and blood osmolarity (ion concentration) is maintained in homeostasis. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.13%3A_Microbial_Diseases_of_the_Genitourinary_System/15.13B%3A_Overview_of_the_Urinary_System.txt |
The vaginal microflora consist mostly of various lactobacillus species.
Learning Objectives
• Recognize the types of bacteria present in the vaginal microflora
Key Points
• If microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate atypical areas of the body (such as through poor hygiene or injury), disease can result.
• Disturbance of the vaginal flora can lead to bacterial vaginosis.
Key Terms
• urinary tract infection: Finding bacteria or other microorganisms, such as yeasts, in bladder urine with or without clinical symptoms and with or without renal disease.
The Genitourinary Microbiome
The human microbiome, or human microbiota, is the aggregate of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. They include bacteria, fungi, and archaea. Some of these organisms perform tasks that are useful for the human host. However, the majority have no known beneficial or harmful effect. Those that are expected to be present and that under normal circumstances do not cause disease, but instead participate in maintaining health, are deemed members of the normal flora.
Populations of microbes inhabit the skin and mucosa. Their role forms part of normal, healthy human physiology; however, if microbe numbers grow beyond their typical ranges (often due to a compromised immune system) or if microbes populate atypical areas of the body (such as through poor hygiene or injury), disease can result.
Proportions of Microbes
It is estimated that 500 to 1000 species of bacteria live in the human gut and a roughly similar number on the skin. Bacterial cells are much smaller than human cells, and there are at least ten times as many bacteria as human cells in the body (approximately 1014 versus 1013). Normal flora bacteria can act as opportunistic pathogens at times of lowered immunity.The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that the most common one is L. iners followed by L. crispatus. Other lactobacilli found in the vagina are L. jensenii, L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to bacterial vaginosis.
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A urinary tract infection (UTI) is an infection affecting the urinary tract; about 150 million people develop UTIs each year.
LEARNING OBJECTIVES
Summarize the various categories of urinary tract infection (UTI): complicated, uncomplicated, upper and lower UTIs
Key Points
• About 150 million people develop a urinary tract infection each year, and they are more common in women than men.
• A urinary tract infection (UTI) is an infection that affects part of the urinary tract. When it affects the lower urinary tract it is known as a bladder infection ( cystitis ); when it affects the upper urinary tract it is known as kidney infection ( pyelonephritis ).
• UTIs are generally treatable with antibiotics, though resistance to some of the medications is growing.
Key Terms
• urinary tract infection: A bacterial infection that affects part of the urinary tract.
About 150 million people develop a urinary tract infection each year. They are more common in women than men. In women, they are the most common form of bacterial infection. Up to 10% of women have a urinary tract infection in a given year and half of women having at least one infection at some point in their lives. They occur most frequently between the ages of 16 and 35 years. Recurrences are common. Urinary tract infections have been described since ancient times with the first documented description in the Ebers Papyrus dated to c. 1550 BC.
A urinary tract infection (UTI) is an infection that affects part of the urinary tract. When it affects the lower urinary tract it is known as a bladder infection (cystitis); when it affects the upper urinary tract it is known as kidney infection (pyelonephritis). Symptoms from a lower urinary tract include pain with urination, frequent urination, and feeling the need to urinate despite having an empty bladder. Symptoms of a kidney infection include fever and flank pain usually in addition to the symptoms of a lower UTI. Rarely the urine may appear bloody. In the very old and the very young, symptoms may be vague or non-specific.
The most common cause of infection is Escherichia coli, though other bacteria or fungi may rarely be the cause. Risk factors include female anatomy, sexual intercourse, diabetes, obesity, and family history. Although sexual intercourse is a risk factor, UTIs are not classified as sexually transmitted infections (STIs). Kidney infection, if it occurs, usually follows a bladder infection but may also result from a blood-borne infection. Diagnosis in young healthy women can be based on symptoms alone. In those with vague symptoms, diagnosis can be difficult because bacteria may be present without there being an infection. In complicated cases or if treatment fails, a urine culture may be useful.
Categories of UTI
Uncomplicated UTIs
In uncomplicated cases, a diagnosis may be made and treatment given based on symptoms alone without further laboratory confirmation, and treatment involves a short course of antibiotics such as nitrofurantoin or trimethoprim / sulfamethoxazole. Resistance to many of the antibiotics used to treat this condition is increasing.
Complicated UTIs
In complicated cases, it may be useful to confirm the diagnosis via urinalysis, looking for the presence of urinary nitrites, white blood cells ( leukocytes ), or leukocyte esterase. Another test, urine microscopy, looks for the presence of red blood cells, white blood cells, or bacteria. A longer course or intravenous antibiotics may be needed. If symptoms do not improved in two or three days, further diagnostic testing may be needed. Phenazopyridine may help with symptoms. In those who have bacteria or white blood cells in their urine but have no symptoms, antibiotics are generally not needed, although during pregnancy is an exception. In those with frequent infections, a short course of antibiotics may be taken as soon as symptoms begin or long term antibiotics may be used as a preventative measure.
Lower UTI
Lower urinary tract infection is also referred to as a bladder infection. The most common symptoms are burning with urination and having to urinate frequently (or an urge to urinate) in the absence of vaginal discharge and significant pain. These symptoms may vary from mild to severe and in healthy women last an average of six days. Some pain above the pubic bone or in the lower back may be present.
Upper UTI
People experiencing an upper urinary tract infection, or pyelonephritis, may experience flank pain, fever, or nausea and vomiting in addition to the classic symptoms of a lower urinary tract infection. Rarely the urine may appear bloody or contain visible pus in the urine.
Prevention
A number of measures have not been confirmed to affect UTI frequency including: urinating immediately after intercourse, the type of underwear used, personal hygiene methods used after urinating or defecating, or whether a person typically bathes or showers. There is similarly a lack of evidence surrounding the effect of holding one’s urine, tampon use, and douching. In those with frequent urinary tract infections who use spermicide or a diaphragm as a method of contraception, they are advised to use alternative methods. In those with benign prostatic hyperplasia urinating in a sitting position appears to improve bladder emptying which might decrease urinary tract infections in this group.
For those with recurrent infections, taking a short course of antibiotics when each infection occurs is associated with the lowest antibiotic use. A prolonged course of daily antibiotics is also effective. Medications frequently used include nitrofurantoin and trimethoprim/sulfamethoxazole (TMP/SMX). Methenamine is another agent used for this purpose as in the bladder where the acidity is low it produces formaldehyde to which resistance does not develop. Some recommend against prolonged use due to concerns of antibiotic resistance. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.14%3A_Bacterial_Diseases_of_the_Urinary_System/15.14A%3A_Urinary_Tract_Infection_%28UTI%29.txt |
Learning Objectives
• Differentiate among the distinct types of cystitis: traumatic, interstitial, eosinophilic, hemorrhagic cystitis, and cystitis cystica, recognizing their causes and risk factors
A urinary tract infection (UTI), a bacterial infection that affects the lower urinary tract, is also known as a simple cystitis (a bladder infection). Symptoms from a lower urinary tract infection include painful urination and either frequent urination or the urge to urinate (or both). Cystitis is a urinary bladder inflammation that can result from any one of a number of distinct syndromes. It is most commonly caused by a bacterial infection in which case it is referred to as a urinary tract infection.
Signs and Symptoms
• Pressure in the lower pelvis
• Painful urination (dysuria)
• Frequent urination (polyuria) or urgent need to urinate (urinary urgency)
• Need to urinate at night (nocturia)
• Urine that contains traces of blood (haematuria)
• Dark, cloudy or strong-smelling urine
• Pain above the pubic bone, or in the lower back or abdomen
• Feeling unwell, weak, or feverish
There are several medically distinct types of cystitis, each having a unique etiology and therapeutic approach:
• Traumatic cystitis is probably the most common form of cystitis in the female. It is due to bruising of the bladder, usually by abnormally forceful sexual intercourse. This is often followed by bacterial cystitis, frequently by coliform bacteria being transferred from the bowel through the urethra into the bladder.
• Interstitial cystitis (IC) is considered more of an injury to the bladder resulting in constant irritation and rarely involves the presence of infection. IC patients are often misdiagnosed with UTI/cystitis for years before they are told that their urine cultures are negative. Antibiotics are not used to treatment of IC. The cause of IC is unknown, although some suspect it may be autoimmune where the immune system attacks the bladder. Several therapies are now available.
• Eosinophilic cystitis (EC) is a rare form of cystitis that is diagnosed via biopsy. In these cases, the bladder wall is infiltrated with a high number of eosinophils. The cause of EC may be attributed to infection by Schistosoma haematobium or by certain medications in afflicted children. Some consider it a form of interstitial cystitis.
• Hemorrhagic cystitis can occur as a side effect of cyclophosphamide, ifosfamide, and radiation therapy. Radiation cystitis, one form of hemorrhagic cystitis is a rare consequence of patients undergoing radiation therapy for the treatment of cancer. Several adenovirus serotypes have been associated with an acute, self-limited hemorrhagic cystitis, which occurs primarily in boys. It is characterized by hematuria, and virus can usually be recovered from the urine. In sexually active women the most common cause of urinary tract infection is from E. coli and Staphylococcus saprophyticus.
• Cystitis cystica is a chronic cystitis glandularis accompanied by the formation of cysts. This disease can cause chronic urinary tract infections. It appears as small cysts filled with fluid and lined by one or more layers of epithelial cells. These are due to hydropic degeneration in center of Brunn’s nests
Key Points
• Cystitis is a urinary bladder inflammation that is most commonly caused by a bacterial infection in which case it is referred to as a urinary tract infection. Symptoms from a lower urinary tract include painful urination and either frequent urination or urge to urinate (or both), but neither may be present.
• Traumatic cystitis is probably the most common form of cystitis in the female. It is due to bruising of the bladder, usually by abnormally forceful sexual intercourse.
• Interstitial cystitis (IC) is considered more of an injury to the bladder resulting in constant irritation and rarely involves the presence of infection.
Key Terms
• cystitis: Cystitis is a urinary bladder inflammation that can result from any one of a number of distinct syndromes. It is most commonly caused by a bacterial infection in which case it is referred to as a urinary tract infection.
15.14C: Pyelonephritis
Learning Objectives
• Identify the main symptoms of pyelonephritis
Pyelonephritis is an inflammation of the kidney tissue, calyces, and renal pelvis. It is commonly caused by bacterial infection that has spread up the urinary tract or travelled through the bloodstream to the kidneys. A similar term is “pyelitis” which means inflammation of the pelvis and calyces. In other words, pyelitis together with nephritis is collectively known as pyelonephritis. Severe cases of pyelonephritis can lead to pyonephrosis (pus accumulation around the kidney), sepsis (a systemic inflammatory response of the body to infection), kidney failure and even death.
Pyelonephritis presents with fever, accelerated heart rate, painful urination, abdominal pain radiating to the back, nausea, and tenderness at the costovertebral angle on the affected side. Pyelonephritis that has progressed to urosepsis may be accompanied by signs of septic shock, including rapid breathing, decreased blood pressure, violent shivering, and occasionally delirium. Pyelonephritis requires antibiotic therapy, and sometimes surgical intervention, as well as treatment of any underlying causes to prevent its recurrence.
Key Points
• Pyelonephritis is an inflammation of the kidney tissue and renal area of the pelvis.
• Pyelonephritis is most commonly caused by a bacterial infection ascending up the upper urinary tract.
• Severe cases of pyelonephritis can lead to sepsis, kidney failure, and death.
• Pyelonephritis presents with fever, accelerated heart rate, painful urination, abdominal pain, and nausea.
• Pyelonephritis requires antibiotic therapy, and sometimes surgical intervention, as well as treatment of any underlying causes to prevent recurrence.
Key Terms
• pyelonephritis: An ascending urinary tract infection that has reached the pelvis or the kidney.
• Urinary tract: The organ system that produces, stores, and eliminates urine. In humans it includes two kidneys, two ureters, the bladder, and the urethra. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.14%3A_Bacterial_Diseases_of_the_Urinary_System/15.14B%3A_Cystitis.txt |
Learning Objectives
• Generalize the causes and mode of transmission for leptospirosis
Leptospirosis (also known as Weil’s Syndrome, canicola fever, canefield fever, nanukayami fever, 7-day fever, Rat Catcher’s Yellows, Fort Bragg fever, black jaundice, and Pretibial fever) is caused by bacteria of the genus Leptospira, and affects humans as well as other animals. Symptoms can range from none to mild such as headaches, muscle pains, and fevers; to severe with bleeding from the lungs or meningitis. If the infection causes the person to turn yellow, have kidney failure and bleeding it is then known as Weil’s disease. If the infection causes lots of bleeding from the lungs it is known as severe pulmonary haemorrhage syndrome.
Leptospirosis is among the world’s most common diseases transmitted to people from animals. The infection is commonly transmitted to humans by allowing water that has been contaminated by animal urine to come in contact with unhealed breaks in the skin, eyes, or mucous membranes. Outside of tropical areas, leptospirosis cases have a relatively distinct seasonality, with most cases occurring in spring and autumn.
Leptospirosis is caused by a spirochaete bacterium called Leptospira spp. There are at least five serotypes of importance in the United States and Canada, all of which cause disease in dogs (Icterohaemorrhagiae, Canicola, Pomona, Grippotyphosa, and Bratislava).There are other (less common) infectious strains as well. Leptospirosis is transmitted by the urine of an infected animal and is contagious as long as it is still moist. Although rats, mice, and moles are important primary hosts, a wide range of other mammals (including dogs, deer, rabbits, hedgehogs, cows, sheep, raccoons, opossums, skunks, and certain marine mammals) are able to carry and transmit the disease as secondary hosts. Dogs may lick the urine of an infected animal off the grass or soil or drink from an infected puddle.
There have been reports of “house dogs” contracting leptospirosis from licking the urine of infected mice that enter the house. The type of habitats most likely to carry infectious bacteria are muddy riverbanks, ditches, gullies, and muddy livestock-rearing areas where there is regular passage of either wild or farm mammals. There is a direct correlation between the amount of rainfall and the incidence of leptospirosis, making it seasonal in temperate climates and year-round in tropical climates. Leptospirosis is also transmitted by the semen of infected animals. Humans become infected through contact with water, food, or soil containing urine from these infected animals. This may result from swallowing contaminated food and water or through skin contact. The disease is not known to be spread from person to person, and cases of bacterial dissemination in convalescence are extremely rare in humans. Leptospirosis is common among water-sport enthusiasts in specific areas, as prolonged immersion in water is known to promote the entry of the bacteria. Surfers and whitewater paddlers are at especially high risk in areas that have been shown to contain the bacteria, and can contract the disease by swallowing contaminated water, splashing contaminated water into their eyes or nose, or exposing open wounds to infected water.
Key Points
• Leptospirosis symptoms can range from none to mild such as headaches, muscle pains, and fevers; to severe with bleeding from the lungs or meningitis.
• Outside of tropical areas, leptospirosis cases have a relatively distinct seasonality, with most cases occurring in spring and autumn.
• Leptospirosis is transmitted by the urine of an infected animal and is contagious as long as it remains moist.
• There is a direct correlation between the amount of rainfall and the incidence of leptospirosis, making it seasonal in temperate climates and year-round in tropical climates.
Key Terms
• leptospirosis: an acute, infectious, febrile disease of both humans and animals, caused by spirochetes of the genus Leptospira
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Prostatitis is an inflammation of the prostate which can be caused by bacteria.
Learning Objectives
• Define the symptoms, diagnostic tests and treatments used for prostatitis
Key Points
• Bacteria can cause acute and chronic prostatitis.
• Acute prostatitis is a serious condition that needs immediate treatment with antibiotics. If treated promptly complications are rare.
• Chronic prostatitis is a rare disease that is harder to treat and has high recurrence rate. In the case of remission, combinations of antibiotics may be a better therapy than a single antibiotic.
Key Terms
• bactericidal: An agent that kills bacteria.
• bacteriostatic: A drug that prevents bacterial growth and reproduction but does not necessarily kill them. When it is removed from the environment the bacteria start growing again.
• cystitis: An inflammation of the urinary bladder.
Prostatitis is an inflammation of the prostate which can be caused by bacteria. Bacterial infections can cause both acute and chronic prostatitis.
Symptoms and diagnosis
Acute prostatitis is relatively easy to diagnose because it presents the general infection symptoms which may include: fever, chills, groin and lower back pain, issues during urination, and general body aches. The prostate is usually enlarged. Testing of urine samples reveals the presence of bacteria and white blood cells. Blood samples can contain bacteria. White blood cells counts are elevated in the complete blood count.
Chronic prostatitis is a rare condition. It usually causes intermittent urinary tract infections (UTIs) which can lead to cystitis. Sometimes there are no symptoms. The diagnosis is made after culturing urine or prostate liquid. Semen analysis can also be used for diagnosis it. PSA (prostate specific antigen) levels may be elevated.
INFECTIOUS AGENTS
Common bacteria that cause acute prostatitis include gram negative bacteria such as Escherichia coli, Klebsiella, Proteus, Enterobacter, Pseudomonas, as well as gram positive bacteria such as Staphylococcus aureus. E. coli is the major infectious agent that causes chronic prostatitis.
TREATMENT
Acute prostatitis is a serious condition that requires immediate treatment to prevent complications such as sepsis. The antibiotics of choice should be bactericidal (e.g., quinolone) not bacteriostatic (e.g., tetracycline) if the infection is life-threatening. Other commonly used antibiotics are doxycycline and ciprofloxacin. Severe infections may require hospitalization, while milder cases (no sepsis) can be treated with antibiotic administration combined with bed rest at home. The infection is usually cured successfully with antibiotics and the recovery is complete without further complications. Treatment of chronic prostatitis requires courses of antibiotic administration for one to two months or a longer course with low doses. The recurrence of the disease is high. In these cases higher success rates of treatment are achieved when a combination of antibiotics is used. Animal studies have shown that E. coli extract with cranberry can prevent chronic prostatitis. The choice of antibiotic for chronic prostatitis also depends on its ability to penetrate the prostatic capsule. Good penetrators of the barrier are quinolones, doxycycline, macrolides and sulfas (Bactrim). In the case of acute prostatitis, the prostate-blood barrier is damaged by the infection so the penetrating ability of the antibiotic is not as important.
15.15B: Prostatitis
Prostatitis is an inflammation of the prostate which can be caused by bacteria.
Learning Objectives
• Define the symptoms, diagnostic tests and treatments used for prostatitis
Key Points
• Bacteria can cause acute and chronic prostatitis.
• Acute prostatitis is a serious condition that needs immediate treatment with antibiotics. If treated promptly complications are rare.
• Chronic prostatitis is a rare disease that is harder to treat and has high recurrence rate. In the case of remission, combinations of antibiotics may be a better therapy than a single antibiotic.
Key Terms
• bactericidal: An agent that kills bacteria.
• bacteriostatic: A drug that prevents bacterial growth and reproduction but does not necessarily kill them. When it is removed from the environment the bacteria start growing again.
• cystitis: An inflammation of the urinary bladder.
Prostatitis is an inflammation of the prostate which can be caused by bacteria. Bacterial infections can cause both acute and chronic prostatitis.
Symptoms and diagnosis
Acute prostatitis is relatively easy to diagnose because it presents the general infection symptoms which may include: fever, chills, groin and lower back pain, issues during urination, and general body aches. The prostate is usually enlarged. Testing of urine samples reveals the presence of bacteria and white blood cells. Blood samples can contain bacteria. White blood cells counts are elevated in the complete blood count.
Chronic prostatitis is a rare condition. It usually causes intermittent urinary tract infections (UTIs) which can lead to cystitis. Sometimes there are no symptoms. The diagnosis is made after culturing urine or prostate liquid. Semen analysis can also be used for diagnosis it. PSA (prostate specific antigen) levels may be elevated.
INFECTIOUS AGENTS
Common bacteria that cause acute prostatitis include gram negative bacteria such as Escherichia coli, Klebsiella, Proteus, Enterobacter, Pseudomonas, as well as gram positive bacteria such as Staphylococcus aureus. E. coli is the major infectious agent that causes chronic prostatitis.
TREATMENT
Acute prostatitis is a serious condition that requires immediate treatment to prevent complications such as sepsis. The antibiotics of choice should be bactericidal (e.g., quinolone) not bacteriostatic (e.g., tetracycline) if the infection is life-threatening. Other commonly used antibiotics are doxycycline and ciprofloxacin. Severe infections may require hospitalization, while milder cases (no sepsis) can be treated with antibiotic administration combined with bed rest at home. The infection is usually cured successfully with antibiotics and the recovery is complete without further complications. Treatment of chronic prostatitis requires courses of antibiotic administration for one to two months or a longer course with low doses. The recurrence of the disease is high. In these cases higher success rates of treatment are achieved when a combination of antibiotics is used. Animal studies have shown that E. coli extract with cranberry can prevent chronic prostatitis. The choice of antibiotic for chronic prostatitis also depends on its ability to penetrate the prostatic capsule. Good penetrators of the barrier are quinolones, doxycycline, macrolides and sulfas (Bactrim). In the case of acute prostatitis, the prostate-blood barrier is damaged by the infection so the penetrating ability of the antibiotic is not as important. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15A%3A_Prostatitis.txt |
Gonorrhea (also colloquially known as the clap) is a common human sexually transmitted infection caused by the bacterium Neisseria gonorrhoeae.
Learning Objectives
• Describe gonorrhea
Key Points
• The usual symptoms of gonorrhea in men are burning with urination and penile discharge.
• Women with gonorrhea, on the other hand, are asymptomatic half the time or have vaginal discharge and pelvic pain.
• If gonorrhea is left untreated, it may spread locally causing epididymitis or pelvic inflammatory disease or throughout the body, affecting joints and heart valves.Treatment is commonly with ceftriaxone as antibiotic resistance has developed to many previously used medications.
Key Terms
• ceftriaxone: A synthetic cephalosporin antibiotic used to treat gonorrhea.
Gonorrhea (also colloquially known as the clap) is a common human sexually transmitted infection. The usual symptoms in men are burning with urination and penile discharge. Women, on the other hand, are asymptomatic half the time or have vaginal discharge and pelvic pain. In both men and women if gonorrhea is left untreated, it may spread locally causing epididymitis or pelvic inflammatory disease or throughout the body, affecting joints and heart valves.Treatment is commonly with ceftriaxone as antibiotic resistance has developed to many previously used medications. In 2011, there were reports of some strains of gonorrhea showing resistance to ceftriaxone. Half of women with gonorrhea are asymptomatic while others have vaginal discharge, lower abdominal pain or pain with intercourse.
The most common male symptoms are urethritis associated with burning with urination and discharge from the penis. Either sex may also acquire gonorrhea of the throat from performing oral sex on an infected partner, usually a male partner. Such infection is asymptomatic in 90% of cases, and produces a sore throat in the remaining 10%. The incubation period is 2 to 14 days with most of these symptoms occurring between 4–6 days after being infected. Rarely, gonorrhea may cause skin lesions and joint infection (pain and swelling in the joints) after traveling through the blood stream. Very rarely it may settle in the heart causing endocarditis or in the spinal column causing meningitis (both are more likely among individuals with suppressed immune systems, however).
CAUSE
Gonorrhea is caused by the bacteria Neisseria gonorrhoeae. The infection is transmitted from one person to another through vaginal, oral, or anal sex. Men have a 20% risk of getting the infection from a single act of vaginal intercourse with an infected woman. The risk for men who have sex with men is higher. Women have a 60–80% risk of getting the infection from a single act of vaginal intercourse with an infected man. A mother may transmit gonorrhea to her newborn during childbirth; when affecting the infant’s eyes, it is referred to as ophthalmia neonatorum. It cannot be spread by toilets or bathrooms.
15.15D: Nongonococcal Urethritis (NGU)
Nongonococcal urethritis (NGU) is an urethral inflammation that is not caused by Neisseria gonorrhoeae.
Learning Objectives
• Recognize the symptoms, causes and treatments for nongonococcal urethritis (NGU)
Key Points
• The general symptoms are pain on urination, frequent urination, and white or cloudy discharge.
• It can be caused by many infectious agents, with the most common being chlamydia.
• Since many different infectious agents can be causing NGU, the initial treatment should be with a broad spectrum antibiotic.
Key Terms
• epididymitis: An inflammation of the epididymis, a structure in the testicles where sperm matures.
Nongonococcal urethritis (NGU) is a urethral inflammation that is not caused by Neisseria gonorrhoeae, a classification used by doctors for treatment purposes. The general symptoms are pain on urination, frequent need to urinate and white or cloudy discharge. The most common symptoms unique to men are discharge from the penis, itching, and tenderness. In women, the symptoms include vaginal discharge, abdominal pain. If irregular menstrual bleeding is present it may indicate that the infection has progressed into pelvic inflammatory disease.
Diagnosing NGU is based on the lack of Neisseria gonorrhoeae in laboratory testsin a patient with urethritis. In men, it can be diagnosed with Gram staining of urethral discharge; the same is not true for women, since they may have other Gram negative bacteria that are part of their normal vaginal microflora. There are multiple infectious agents that can cause nongonococcal inflammation of the urethra. The most common bacterial agent is Chlamydia trachomatis (about a quarter to half of all NGU cases), though others include Ureaplasma urealyticum, Haemophilus vaginalis and Mycoplasma genitalium. Viral infections can be caused sometimes by the Herpes simplex virus or adenovirus. Parasites such as Trichomonas vaginalis can cause inflammation too, although rarely. NGU can be caused by reasons different than infection, such as the use of some chemicals or physical injuries. Since many different infectious agents can be causing NGU, the initial treatment should be with a broad spectrum antibiotic. Studies indicate that therapies with doxycycline or azithromycin with tinidazole can be more effective than doxycycline or azithromycin alone. Sexual partners of infected patients should be treated as well. Prompt treatment is critical in both men and women. Women are at risk of developing pelvic inflammatory disease (PID), while in men the infection can progress to epididymitis and cause infertility.
15.15E: Pelvic Inflammatory Disease (PID)
Pelvic inflammatory disease (PID) is an inflammation of the female reproductive organs that is most often caused by infection.
Learning Objectives
• Describe the causes, symptoms and long-term effects of pelvic inflammatory disease
Key Points
• Different agents can cause the infection but the most common are Chlamydia trachomatis and Neisseria gonorrhoeae.
• PID can cause permanent damage to the affected organs leading to issues such as infertility and chronic pelvic pain.
• Single antibiotics or combinations of antibiotics are used for the treatment of PID.
Key Terms
• ectopic: Being out of place, such as a pregnancy occurring inside the fallopian tubes instead of the uterus.
• pelvic inflammatory disease: inflammation of the uterus, fallopian tubes, and/or ovaries as it progresses to scar formation with adhesions to nearby tissues and organs
• asymptomatic: not exhibiting any symptoms of disease.
Pelvic inflammatory disease (PID) is an inflammation of the uterus, fallopian tubes and/or the ovaries. It is most often caused by a sexually transmitted infection (STI) but there are other predisposing conditions (e.g., postpartum period, the use of intrauterine device). It should be treated promptly to avoid serious complications like scarring and adhesions which can cause infertility, ectopic pregnancy and chronic pelvic pain.
Symptoms and diagnosis
PID can be asymptomatic or present with acute symptoms. About two thirds of patients whose laparoscopies indicated a previous PID were unaware of it. Asymptomatic infections should be treated as well, since they can still cause permanent damage to the reproductive tract.
Symptoms include fever, lower abdominal pain, unusual discharge, irregular menstrual bleeding, painful intercourse.
Different tests can be used for diagnosis such as pelvic ultrasound and laboratory tests for STIs. Usually, more than one test is needed for proper diagnosis. Early diagnosis and treatment are critical to limit the spread of the infection to the lower part of the tract and to avoid long term consequences.
Infectious agents
PID can be caused by many different infectious agents like viruses, fungi or bacteria. The most common infectious agents are Chlamydia trachomatis and Neisseria gonorrhoeae which are sexually transmitted.
The normal vaginal flora can also cause PID under certain circumstances. Co-infection with multiple species is also possible.
Treatment
The primary mode of therapy is an antibiotic regimen. In serious cases, intravenous administration of drugs may be necessary. Usually, improvement of symptoms should be noticed within a few days.
Sexual partners of patients with PID should be treated as well. Some of the most commonly used antibiotics and combinations of antibiotics are: cefoxitin or cefotetan plus doxycycline, cefoxitin plus doxycycline, clindamycin plus gentamycin, ampicillin and sublactam plus doxycycline. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15C%3A_Gonorrhea.txt |
Learning Objectives
• Describe syphilis, its affect on the spinal cord, and its methods of transmission
Syphilis is a sexually transmitted infection (STI) caused by the spirochete bacterium Treponema pallidum.
FOUR STAGES OF SYPHILIS
The signs and symptoms of syphilis vary depending on which of the four stages it presents (primary, secondary, latent, or tertiary). The primary stage classically presents itself with a single chancre (a firm, painless, non-itchy skin ulceration) as shown in. Secondary syphilis shows itself with a diffuse rash that frequently involves the palms of the hands and soles of the feet. Latent syphilis displays little to no symptoms, and neurosyphilis (tertiary) can result in neurological and cardiac symptoms because the syphilis has been undiagnosed or untreated for many years.
DIAGNOSIS AND TREATMENT
Diagnosis is usually via blood tests, but the bacteria can also be visualized under a microscope. Syphilis can be effectively treated with antibiotics, specifically the preferred intramuscular penicillin G (given intravenously for neurosyphilis), or else ceftriaxone, and in those who have a severe penicillin allergy, oral doxycycline or azithromycin.
Syphilis is believed to have infected 12 million people globally in 1999, with more than 90 percent of cases in the developing world. Rates decreased dramatically after the widespread availability of penicillin in the 1940s. However, rates of infection have increased since the turn of the century in many countries, often in combination with human immunodeficiency virus (HIV). By some accounts, this has been attributed, in part, to unsafe sexual practices among men who have sex with men, increased promiscuity among all genders, prostitution, and decreasing use of barrier protection.
PRIMARY SYPHILIS
Primary syphilis is typically acquired by direct sexual contact with the infectious lesions of another person. Approximately three to 90 days after the initial exposure (average 21 days) a skin lesion, called a chancre, appears at the point of contact. This chancre is classically a single, firm, painless, non-itchy skin ulceration with a clean base and sharp borders between 0.3 and 3.0 cm in size. However, the lesion may take on almost any form. In the classic form, it evolves from a macule to a papule and finally to an erosion or ulcer. Occasionally, multiple lesions may be present, with multiple lesions more common when co-infected with HIV. Lesions may be painful or tender (in 30 percent of those infected), and they may occur outside of the genitals (2 to 7 percent). The lesion may persist for three to six weeks without treatment.
SECONDARY SYPHILIS
Secondary syphilis occurs approximately four to 10 weeks after the primary infection. While secondary disease is known for the many different ways it can manifest, symptoms most commonly involve the skin, mucous membranes, and lymph nodes. There may be a symmetrical, reddish-pink, non-itchy rash on the trunk and extremities, including the palms and soles of the feet. The rash may become maculopapular or pustular. It may form flat, broad, whitish, wart-like lesions known as condyloma latum on mucous membranes. All of these lesions harbor bacteria and are infectious.
Other symptoms may include fever, sore throat, malaise, weight loss, hair loss, and headache. Rare manifestations include hepatitis, kidney disease, arthritis, periostitis, optic neuritis, uveitis, and interstitial keratitis. The acute symptoms usually resolve after three to six weeks; however, about 25 percent of people may experience a recurrence of secondary symptoms.
NEUROSYPHILIS
Neurosyphilis occurs when syphilis is left untreated from many years. The brain and spinal cord become infected with the syphilis bacterium, Treponema pallidum, during the secondary stage of infection and can remain latent for 10 to 20 years after the initial infection. Eventually, this infection begins to damage the tissues of the brain and spinal cord, resulting in neurosyphilis. Neurosyphilis is characterized by neurological and psychiatric symptoms, such as confusion, blindness, abnormal gait and dementia. Left untreated, neurosyphilis symptoms will worsen over time and can lead to death. Treatment for neurosyphilis is the same as any other stage of syphilis, requiring only a short course of penicillin.
TRANSMISSION AND PREVENTION
Syphilis is transmitted primarily by sexual contact or during pregnancy from a mother to her fetus. The spirochete is able to pass through intact mucous membranes or compromised skin. Therefore, it is transmissible by kissing, or oral, vaginal, and anal sex. Approximately 30 to 60 percent of those exposed to primary or secondary syphilis will get the disease. It can be transmitted via blood products, but, many countries test for it, and thus the risk is low. The risk of transmission from sharing needles appears limited. Syphilis cannot be contracted through toilet seats, daily activities, hot tubs, or sharing eating utensils or clothing.
As of 2010, there is no vaccine effective for prevention. Abstinence from intimate physical contact with an infected person is effective at reducing the transmission of syphilis, as is the proper use of a latex condom. However, condom use does not completely eliminate the risk.
Key Points
• In addition to sexual contact, syphilis may also be transmitted from mother to child during pregnancy or at birth, resulting in congenital syphilis.
• Primary syphilis is typically acquired by direct sexual contact with the infectious lesions of another person, and usually presents with a single skin ulceration called a chancre.
• Secondary syphilis occurs approximately four to 10 weeks after the primary infection and may present as a symmetrical, reddish-pink, non-itchy rash on the trunk and extremities, including the palms and soles of the feet.
• Primary syphilis typically presents with a single skin ulceration called a chancre.
• Neurosyphilis refers to a syphilis infection that affects the central nervous system, and cardiovascular syphilis affects the cardiovascular system.
• Blood tests for syphilis are either treponemal or nontreponemal.
• The Tuskegee syphilis study, where African American men in rural Alabama were told they were receiving free health care and instead were given syphilis in order to study its symptoms and progression, is one of the most infamous cases of questionable medical ethics in US history.
Key Terms
• congenital syphilis: syphilis present in utero and at birth
• Treponema pallidum: A Gram-negative spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws.
• chancre: A skin lesion, sometimes associated with certain contagious diseases like syphilis.
• syphilis: a disease spread via sexual activity, caused by the bacterium Treponema pallidum
• syphilis: A disease spread via sexual activity, caused by the bacterium Treponema pallidum. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15F%3A_Syphilis.txt |
Genital ulcers are skin ulcers on the genital area caused by sexually transmitted diseases or noninfectious conditions.
Learning Objectives
• List the causes and symptoms of genital ulcers
Key Points
• The most common STDs that present with genital ulcers are genital herpes, syphilis, chlamydia and chancroid.
• Other than ulceration, enlarged lymph nodes in the groin area may be present, along with blisters and sores.
• To improve the outcome, treatment often starts before identification is complete, with medications chosen based on symptoms and epidemiological circumstances.
Key Terms
• Behcet’s syndrome: Behcet’s syndrome, or Behcet’s disease, is an immune disorder that leads to inflammation of the blood vessels. Common symptoms include mouth and genital ulcers, as well as ocular issues.
Genital ulcers are skin ulcers located on the genital area and can be caused by a number of sexually transmitted diseases or other noninfectious conditions such as yeasts, trauma, lupus, rheumatoid arthritis or Behcet’s syndrome.
Sexually Transmitted Genital Ulcers
When the reason for a genital ulcer is an infection, it can be caused by a number of sexually transmitted diseases. Among the most common are Herpes simplex virus (HSV), the genital herpes agent; Treponema pallidum, that causes syphilis; Chlamydia trachomatis, the cause of chlamydia; and Haemophilus ducreyi, the chancroid agent. In the United States, the most common reasons for genital ulcers in young and sexually active patients are genital herpes and syphilis.
Symptoms and Diagnosis
Genital ulcers can be painful or painless depending on the type of infection. Their appearance can be slightly different from one disease to another. Other than ulceration, enlarged lymph nodes in the groin area can be present, along with blisters and sores. Proper diagnosis cannot be obtained solely through examination and medical history. Testing for a specific infectious agent depends on the likelihood of its presence. In the U.S., testing is recommended for syphilis (by serology and darkfield microscopy) and HSV (culture, serology or PCR), and in cases of chancroid outbreaks or based on the medical history, for the presence of Haemophilus ducreyi. In about 25% of the cases, the reason for the ulcer will not be identified by laboratory testing. Syphilis, genital herpes and chancroid have all been associated with increasing the risk for HIV transmission. The CDC recommends routine HIV screening for all patients who present with genital ulcers.
Treatment
Since the ulcers are symptoms of a number of infectious agents, the treatment is chosen according to the disease agent if it can be identified. Quite often, therapy has to start before identification is complete in order to decrease the chances for transmission and to increase the probability of successful treatment. The choice of medication is made, after careful examination of the symptoms and all epidemiological circumstances, based on the most likely causative agent.
15.15H: Lymphogranuloma Venereum
Lymphogranuloma venereum (LGV) is a sexually transmitted disease which causes an infection of the lymph nodes.
Learning Objectives
• Outline the causes and disease stages for lymphogranuloma venereum (LGV)
Key Points
• The infectious agents are a few serovars of Chlamydia trachomatis: L1, L2, L2a, L2b and L3.
• The symptoms of LGV include enlarged and inflamed lymph nodes and lymph passages as well as infection of the surrounding tissues in the genital and abdominal areas.
• Treatment of LGV includes antibiotics and may require drainage of inflamed nodes.
Key Terms
• serovar: A group of microorganisms (viruses or bacteria), belonging to the same species, that are characterized by the presence of a specific antigen on their surface.
• bubo: An inflamed swelling of a lymph node, especially in the armpit or the groin, due to an infection such as bubonic plague, gonorrhea, tuberculosis or syphilis.
Lymphogranuloma venereum (LGV) is a sexually transmitted disease which was considered rare in the developed world until about a decade ago. LGV is an infection of the lymph nodes. The infectious agent enters the body through breaks in the skin or through the epithelial layer of mucous membranes.
Infectious Agents
The infectious agents are a few serovars of Chlamydia trachomatis: L1, L2, L2a, L2b and L3.
Symptoms and Diagnosis
The general symptoms may include fever, malaise and decreased appetite. The disease progresses in stages. In the primary stage, symptoms appear within days after infection. The first symptom is usually painless ulcers at the contact area.The secondary stage can manifest from days to months later. The infectious agent spreads to the lymph nodes through the lymphatic drainage pathways, causing inflammation of the lymph nodes and lymphatic channels. In males with genital infection, these symptoms will usually be in the inguinal or/and femoral areas. In women, an inflammation of the cervix, the fallopian tubes or/and peritonitis may appear as well as inflammation and infection of the lymphatic system. If the infection started in the anal area, it may cause inflammation of the rectum or the colonic mucosa, presenting with symptoms such as anorectal pain, discharge, abdominal cramps and diarrhea.
The enlarged lymph nodes are called buboes and are painful, inflamed and can fixate to the skin. These changes can further progress to necrosis, abscesses and fistulas. As healing starts, fibrosis may occur in the inflamed areas and cause obstruction of the lymphatic system and edema. The fibrosis and edema are considered the third stage of LGV and are mainly permanent. Diagnosis is made after serological analysis and exclusion of other reasons for genital ulcers and lymphatic issues. Culturing is also used for identification of serotypes. Other tests include direct fluorescent antibody analysis (DFA) and PCR tests.
Treatment
Treatment is performed with antibiotics, usually tetracycline, doxycycline or erythromycin. Sometimes drainage of the buboes or abscesses is performed as well. Prognosis is best if treatment starts early in the infection process. Severe complications include bowel obstruction or perforation, which can lead to death. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15G%3A_Genital_Ulcer_Diseases.txt |
Group B streptococcus is part of the natural microflora in some people, but can sometimes cause life-threatening infections.
Learning Objectives
• Describe the pathogenic characteristics, symptoms and diagnostic test used for Group B streptococcus (GBS)
Key Points
• The most vulnerable groups of people to infection are newborns, the elderly, and people with compromised immune system.
• To prevent infections in infants, many countries routinely screen pregnant women for GBS in the third trimester.
• GBS infection is treated with antibiotics, with penicillin and ampicillin as the primary choice.
Key Terms
• sepsis: A life-threatening medical condition caused by a severe inflammatory response of the human body triggered by the presence of an infectious agent.
Group B Streptococcus Colonization
Group B streptococcus (GBS), also called streptococcus agalactiae or simply strep B, is part of the natural genital and intestinal microflora in some people. Studies indicate that as many as 40% of women can be carriers. It is usually harmless but under certain circumstances (in newborns, the elderly, and in people with compromised immune systems) it can cause life-threatening infections. The bacteria is gram-positive streptococcus, and possesses the group B antigen from the Lancefield classification. Its infectivity is due to the presence of a antiphagocytic polysaccharide capsule. If a pregnant woman is a carrier of strep B, the baby can become infected during vaginal delivery.
Symptoms and diagnosis
Healthy adults are usually asymptomatic carriers of the bacteria. Sometimes it can manifest with urinary tract infections (UTIs) in both pregnant and nonpregnant women. In newborns, the first symptoms are breathing difficulties and pneumonia, which can progress to meningitis and sepsis. In elderly people, it can cause pneumonia and/or UTI and is linked to congestive heart failure. A number of different tests are used as diagnostic tools. Screening pregnant women for GBS, usually in the third trimester, is currently routine in many countries. In the cases of positive status, antibiotics are administered during labor to substantially lower the risk of infection for the baby. This strategy has lead to a significant drop in the rates of infant infection in these countries. A very common diagnostic test is the CAMP test named after the three people that discovered it. Sometimes, before plating, enrichment of the gathered probe is performed. This includes sample growth in special medium that will favor its growth over the other bacteria collected with the specimen. The method of enrichment followed by the CAMP tests is currently the gold standard for GBS diagnosis. It lowers significantly the rates of false negatives. However, culturing takes days and is not feasible if labor starts before screening was completed or in cases when it was not performed at all. The best diagnostic tool will allow identification during labor. PCR techniques are faster but they are still complicated and not fast enough to be used widely for diagnostics once labor has started. TreatmentPregnant women who are carriers of GBS are administered penicillin or ampicillin during labor. These antibiotics are the primary choice for GBS therapy in general, since the bacteria are becoming increasingly resistant to many other common antibiotics. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15I%3A_Group_B_Streptococcus_Colonization.txt |
Chancroid is a sexually transmitted disease caused by Haemophilus ducreyi.
Learning Objectives
• Recognize the symptoms, causes and treatment for chancroid
Key Points
• Chancroid is becoming rarer worldwide but there are sporadic outbreaks even in countries where it is uncommon.
• The most common symptoms for chancroid are enlarged lymph nodes and painful, bleeding ulcers with distinctive characteristics.
• Chancroid is treated with single doses of antibiotics like azythromycin or ceftriaxone, or with erythromycin for a week.
Key Terms
• fastidious: Microorganisms that are difficult to culture since they need specific nutrients in their medium to grow.
• lymphadenopathy: An abnormal enlargement of the lymph nodes
Chancroid (soft chancre) is a sexually transmitted disease and can only be spread through sexual contact. It is becoming rarer worldwide with sporadic outbreaks in countries where it is uncommon. This disease is a risk factor for HIV infection.
Infectious Agent
Chancroid is caused by Haemophilus ducreyi, a gram-negative fastidious organism. It enters the body through breaks in the skin.
Symptoms and Diagnosis
The incubation period of chancroid is between one to fourteen days. The area of infection gets inflamed as cells of the immune system gather to fight the invading organism. Between 30-60% of the patients can also develop lymphadenopathy. Quite often, these enlarged lymph nodes can rupture through the skin and produce draining abscesses.The first symptoms after infection are small painless bumps which quickly become painful ulcers. These ulcers can be quite different in size. The base of the ulcers is usually covered in a gray or yellow substance and bleeds easily. They are typically located in specific ares for men and women. Men often have only one ulcer while women present with multiple ulcers. Women have other symptoms as well such as pain during urination and intercourse. For proper diagnosis, the other two infectious agents that can present with similar although not identical ulcers need to be excluded. Tests for the identification of Treponema pallidium (causes syphilis) and HSV (Herpes Simplex Virus, type 2) may be performed to exclude the possibility that ulcers are caused by those agents instead of Haemophilus ducreyi. For identification, samples from patients are cultured on chocolate agar. Even though serological and genetic tests can be used for identification, they are not widely used and culturing is the main tool for identifying Haemophilus ducreyi.
Treatment
Chancroid is treated with single doses of antibiotics like azythromycin or ceftriaxone, or with erythromycin for a week.
15.15K: Bacterial Vaginosis
Bacterial vaginosis (BV) is a condition of disrupted balance of the vaginal microflora.
Learning Objectives
• Describe the symptoms, causes and methods of diagnosis for bacterial vaginosis
Key Points
• The most common symptom is white or gray discharge, that can be thin, with fish-like odor (especially strong after intercourse).
• Common bacterial species that can overgrow and cause symptoms of BV are Gardnerella vaginalis, Mobiluncus, Bacteroides and Mycoplasma.
• The treatment regimen is most often metronidizole (for seven days) or clindamycin. BV has high recurrence rates.
Key Terms
• recurrence: The returning of a disease that was already treated successfuly.
Bacterial vaginosis (BV) is a condition where the vaginal microflora in women have become disrupted. BV is not a typical sexually transmitted disease since women who have never had sexual contact can suffer from this condition, too. However, having sex with a new partner or multiple partners increases the risk of getting BV but it is unclear how and why that happens. BV is a very common condition and it is estimated that about 1 in 3 women will develop it in their lifetime.
Symptoms and diagnosis
Bacterial vaginosis may be completely asymptomatic. The most common symptom is white or gray discharge, that can be thin, with fish-like odor (especially strong after intercourse). Sometimes itching outside of the vagina or/and burning during urination can also be present. For diagnosis in the clinical practice, a swab from the vaginal wall is obtained and examined with a few different tests called the Amsel criteria:
• the discharge should be thin, white, yellow and homogenous
• clue cells must be present in the specimen when observed under the microscope
• pH > 4.5
• the release of fishy odor after the addition of 10% KOH to the specimen
At least three of these tests have to be positive for conclusive diagnosis. Alternative tests can be performed as well and they usually involve Gram staining of the specimen and observing the types of bacteria present in it. Infectious agentsThe normal vaginal microflora contains many species with Lactobacillus as the dominant representative. Some Lactobacilli produce hydrogen peroxide which can prevent the overgrowth of bacteria that will disturb the balance and cause BV. Some of the bacteria that will produce BV symptoms are Gardnerella vaginalis, Mobiluncus, Bacteroides, and Mycoplasma. Factors that are known to disturb the balance are: antibiotics, pH imbalance (douching can alter vaginal pH), psychosocial stress, iron deficiency anemia in pregnant women and women with STD.
Women who already have BV are at increased risk for sexually transmitted diseases including HIV. Bacterial vaginosis during pregnancy increases the risk of premature birth. TreatmentThe treatment regimen is most often metronidizole (for seven days) or clindamycin. The treatment is usually successful but BV has high rates of recurrence. Treatment of male sex partners is usually not recommended but BV can be transferred to female sex partners. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.15%3A_Bacterial_Diseases_of_the_Reproductive_System/15.15J%3A_Chancroid_%28Soft_Chancre%29.txt |
Chlamydia infection is a common sexually transmitted infection (STI) in humans caused by the bacterium Chlamydia trachomatis.
Learning Objectives
• Describe the effects of chlamydia in men and women
Key Points
• Chlamydia infection is one of the most common sexually transmitted infections worldwide; it is estimated that about 1 million individuals in the United States are infected with chlamydia.
• Between half and three-quarters of all women who have a chlamydia infection of the cervix (cervicitis) have no symptoms and do not know that they are infected.
• C. trachomatis infection can be effectively cured with antibiotics once it is detected. Current guidelines recommend azithromycin, doxycycline, erythromycin, or ofloxacin.Agents recommended for pregnant women include erythromycin or amoxicillin.
Key Terms
• azithromycin: A macrolide antibiotic derived from erythromycin.
• sexually transmitted disease: any of various diseases that are usually contracted through sexual contact
Chlamydia infection (from the Greek meaning “cloak”) is a common sexually transmitted infection (STI) in humans caused by the bacterium Chlamydia trachomatis. The term Chlamydia infection can also refer to infection caused by any species belonging to the bacterial family Chlamydiaceae. C. trachomatis is found only in humans.
Chlamydia is a major infectious cause of human genital and eye disease. Chlamydia infection is one of the most common sexually transmitted infections worldwide; it is estimated that about 1 million individuals in the United States are infected with chlamydia. C. trachomatis is naturally found living only inside human cells. Chlamydia can be transmitted during vaginal, anal, or oral sex, and can be passed from an infected mother to her baby during vaginal childbirth. Between half and three-quarters of all women who have a chlamydia infection of the cervix (cervicitis) have no symptoms and do not know that they are infected. In men, infection of the urethra (urethritis) is usually symptomatic, causing a white discharge from the penis with or without pain on urinating (dysuria).
Occasionally, the condition spreads to the upper genital tract in women (causing pelvic inflammatory disease ) or to the epididymis in men (causing epididymitis). If untreated, chlamydial infections can cause serious reproductive and other health problems with both short-term and long-term consequences.
Genital disease
Chlamydial cervicitis in a female patient characterized by mucopurulent cervical discharge, erythema, and inflammation. Male patients may develop a white, cloudy or watery discharge from the tip of the penis.
Women
Chlamydial infection of the neck of the womb (cervicitis) is a sexually transmitted infection which is asymptomatic for about 50-70% of women infected with the disease. The infection can be passed through vaginal, anal, or oral sex. Of those who have an asymptomatic infection that is not detected by their doctor, approximately half will develop pelvic inflammatory disease (PID), a generic term for infection of the uterus, fallopian tubes, and/or ovaries. PID can cause scarring inside the reproductive organs, which can later cause serious complications, including chronic pelvic pain, difficulty becoming pregnant, ectopic (tubal) pregnancy, and other dangerous complications of pregnancy.Chlamydia is known as the “Silent Epidemic” because in women, it may not cause any symptoms in 75% of cases, and can linger for months or years before being discovered. Symptoms that may occur include unusual vaginal bleeding or discharge, pain in the abdomen, painful sexual intercourse (dyspareunia), fever, painful urination or the urge to urinate more frequently than usual (urinary urgency).
Men
In men, chlamydia shows symptoms of infectious urethritis (inflammation of the urethra) in about 50% of cases. Symptoms that may occur include: a painful or burning sensation when urinating, an unusual discharge from the penis, swollen or tender testicles, or fever. Discharge, or the purulent exudate, is generally less viscous and lighter in color than for gonorrhea. If left untreated, it is possible for chlamydia in men to spread to the testicles causing epididymitis, which in rare cases can cause sterility if not treated within 6 to 8 weeks. Chlamydia is also a potential cause of prostatitis in men, although the exact relevance in prostatitis is difficult to ascertain due to possible contamination from urethritis.
Treatment
C. trachomatis infection can be effectively cured with antibiotics once it is detected. Current guidelines recommend azithromycin, doxycycline, erythromycin, or ofloxacin. Agents recommended for pregnant women include erythromycin or amoxicillin.
An option for treating partners of patients ( index cases ) diagnosed with chlamydia or gonorrhea is patient-delivered partner therapy(PDT or PDPT), which is the clinical practice of treating the sex partners of index cases by providing prescriptions or medications to the patient to take to his/her partner without the health care provider first examining the partner.
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Herpes genitalis (or genital herpes) refers to a genital infection by Herpes simplex virus.
Learning Objectives
• Recognize the causes and symptoms of herpes simplex virus (HSV) 1 and 2
Key Points
• Although genital herpes is largely believed to be caused by HSV-2, genital HSV-1 infections are increasing and now exceed 50% in certain populations.
• In males, symptoms of genital herpes include lesions that occur on the glans penis, shaft of the penis or other parts of the genital region, on the inner thigh, buttocks, or anus. In females, lesions appear on or near the pubis, labia, clitoris, vulva, buttocks or anus.
• Presently, genital herpes cannot be cured. Moreover, genital herpes can be transmitted by viral shedding prior to and following the visual signs of symptoms. There are however some drugs that can shorten outbreaks and make them less severe or even stop them from happening.
Key Terms
• acyclovir: An antiviral drug used in the treatment of genital herpes.
• viral shedding: the successful reproduction, expulsion, and host-cell infection caused by virus progeny.
Herpes genitalis (or genital herpes) refers to a genital infection by Herpes simplex virus. Following the classification HSV into two distinct categories of HSV-1 and HSV-2 in the 1960s, it was established that “HSV-2 was below the waist, HSV-1 was above the waist”.
Although genital herpes is largely believed to be caused by HSV-2, genital HSV-1 infections are increasing and now exceed 50% in certain populations, and that rule of thumb no longer applies. HSV is believed to be asymptomatic in the majority of cases, thus aiding contagion and hindering containment. When symptomatic, the typical manifestation of a primary HSV-1 or HSV-2 genital infection is clusters of genital sores consisting of inflamed papules and vesicles on the outer surface of the genitals, resembling cold sores. These usually appear 4–7 days after sexual exposure to HSV for the first time. Genital HSV-1 infection recurs at rate of about one sixth of that of genital HSV-2.
In males, the lesions occur on the glans penis, shaft of the penis or other parts of the genital region, on the inner thigh, buttocks, or anus. In females, lesions appear on or near the pubis, labia, clitoris, vulva, buttocks or anus. Other common symptoms include pain, itching, and burning. Less frequent, yet still common, symptoms include discharge from the penis or vagina, fever, headache, muscle pain (myalgia), swollen and enlarged lymph nodes and malaise. Women often experience additional symptoms that include painful urination (dysuria) and cervicitis. Herpetic proctitis (inflammation of the anus and rectum) is common for individuals participating in anal intercourse.After 2–3 weeks, existing lesions progress into ulcers and then crust and heal, although lesions on mucosal surfaces may never form crusts. In rare cases, involvement of the sacral region of the spinal cord can cause acute urinary retention and one-sided symptoms and signs of myeloradiculitis (a combination of myelitis and radiculitis): pain, sensory loss, abnormal sensations (paresthesia) and rash. Historically this has been termed Elsberg syndrome, although this entity is not clearly defined.
Treatment
Medical research has not been able to find a way to halt the spread of herpes and the number of infected people keeps growing. In the United States alone, 45 million people are infected, with an additional one million new infections occurring every year. Presently, genital herpes cannot be cured. Moreover, genital herpes can be transmitted by viral shedding prior to and following the visual signs of symptoms. There are however some drugs that can shorten outbreaks and make them less severe or even stop them from happening.
Among these drugs are: acyclovir, valacyclovir and famciclovir.Acyclovir is an antiviral drug used against herpes viruses, varicella-zoster, and Epstein-Barr Viruses. This drug reduces the pain and the number of lesions in the initial case of genital herpes. Furthermore, it decreases the frequency and severity of recurrent infections. It comes in capsules, tablets, suspension, injection, powder for injection, and ointment. The ointment is used topically and it decreases pain, reduces healing time, and limits the spread of the infection.Valacyclovir is also used to treat herpes virus infections. Once in the body, it becomes the anti-herpes medicine, acyclovir. It helps relieve the pain and discomfort and the sores heal faster. It only comes in caplets and its advantage is that it has a longer duration of action than acyclovir. Famciclovir is another antiviral drug that belongs to the same class of acyclovir and valacyclovir. Famciclovir is a prodrug that is converted to penciclovir in the body. The latter is the one active against the viruses. This drug has a longer duration of action than acyclovir and it only comes in tablets. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.16%3A_Viral_Diseases_of_the_Reproductive_System/15.16A%3A_Genital_Herpes.txt |
Genital warts is a highly contagious sexually transmitted disease caused by some sub-types of human papillomavirus (HPV).
Learning Objectives
• List the causes and various management procedures for genital warts
Key Points
• Warts are the most easily recognized symptom of genital HPV infection, where types 6 and 11 are responsible for 90% of genital warts cases.
• Genital warts spread through direct skin-to-skin contact during oral, genital, or anal sex with an infected partner.
• Genital warts, histopathologically, characteristically rise above the skin surface due to enlargement of the dermal papillae, have parakeratosis and the characteristic nuclear changes typical of HPV infections (nuclear enlargement with perinuclear clearing).
• There is no cure for HPV, but there are methods to treat visible warts, which could reduce infectivity, although there are no trials studying the effectiveness of removing visible warts in reducing transmission.
Key Terms
• human papillomavirus: A virus that affects humans, sometimes causing cervical or other cancer; it is sometimes classified as a sexually transmitted disease.
Genital warts (or Condylomata acuminata, venereal warts, anal warts and anogenital warts) is a highly contagious sexually transmitted disease caused by some sub-types of human papillomavirus (HPV ). It is spread through direct skin-to-skin contact during oral, genital, or anal sex with an infected partner. Throat, mouth, and eye genital warts can also be transmitted through oral, genital, or anal sex. Warts are the most easily recognized symptom of genital HPV infection, where types 6 and 11 are responsible for 90% of genital warts cases.
Although it is estimated that only a “small percentage” (between 1% and 5%) of those infected with genital HPV develop genital warts, those infected can still transmit the virus. Other types of HPV also cause cervical cancer and probably most anal cancers, however it is important to underline that the types of HPV that cause the overwhelming majority of genital warts are not the same as those that can potentially increase the risk of genital or anal cancer. HPV prevalence at any one time has been observed in some studies at 27% over all sexually active people, rising to 45% between the ages of 14 and 19.
Diagnosis
Genital warts, histopathologically, characteristically rise above the skin surface due to enlargement of the dermal papillae, have parakeratosis and the characteristic nuclear changes typical of HPV infections (nuclear enlargement with perinuclear clearing).
Prevention
Gardasil (sold by Merck & Co.) is a vaccine that protects against human papillomavirus types 16, 18, 6, and 11. Types 6 and 11 cause genital warts, while 16 and 18 cause cervical cancer. The vaccine is preventive, not therapeutic, and must be given before exposure to the virus type to be effective, ideally before the beginning of sexual activity. The vaccine is widely approved for use by young women, it is being tested for young men, and has been approved for males in some areas, such as the UK, the US and Canada.
Management
There is no cure for HPV, but there are methods to treat visible warts, which could reduce infectivity, although there are no trials studying the effectiveness of removing visible warts in reducing transmission. Every year, Americans spend \$200 million on the treatment of genital warts. Genital warts may disappear without treatment, but sometimes eventually develop a fleshy, small raised growth. There is no way to predict whether they will grow or disappear.
Warts can sometimes be identified because they show up as white when acetic acid is applied, but this method is not recommended on the vulva because microtrauma and inflammation can also show up as acetowhite. Magnifying glasses or colposcope may also be used to aid in identifying small warts. Depending on the sizes and locations of warts (as well as other factors), a doctor will offer one of several ways to treat them. Podofilox is the first-line treatment due to its low cost.Almost all treatments can potentially cause depigmentation or scarring. A 0.15% – 0.5% podophyllotoxin (also called podofilox) solution in a gel or cream. Marketed as Condylox (0.5%), Wartec (0.15%) and Warticon (0.15%), it can be applied by the patient to the affected area and is not washed off. It is the purified and standardized active ingredient of the podophyllin (see below). Podofilox is safer and more effective than podophyllin. Skin erosion and pain are more commonly reported than with imiquimod and sinecatechins. Its use is cycled (2 times per day for 3 days then 4–7 days off); one review states that it should only be used for four cycles.
Imiquimod (Aldara) is a topical immune response cream, applied to the affected area. It causes less local irritation than podofilox but may cause fungal infections (11% in package insert) and flu-like symptoms (less than 5% disclosed in package insert). Sinecatechins (marketed as Veregen and Polyphenon E) is an ointment of catechins (55% epigallocatechin gallate) extracted from green tea and other components. Mode of action is undetermined. It appears to have higher clearance rates than podophyllotoxin and imiquimod and causes less local irritation, but clearance takes longer than with imiquimod. Liquid nitrogen cryosurgery is safe for pregnancy. It kills warts 71–79% of the time, but recurrence is 38% to 73% 6 months after treatment. Local infections have been reported. Trichloroacetic acid (TCA) is less effective than cryosurgery, and is not recommended for use in the vagina, cervix, or urinary meatus. Surgical excision is best for large warts, and has a greater risk of scarring. Laser ablation does not seem to be any more effective than other physician-applied methods, but is often used as a last resort and is extremely expensive. A 20% podophyllin anti-mitotic solution, applied to the affected area and later washed off. However, this crude herbal extract is not recommended for use on vagina, urethra, perianal area, or cervix, and must be applied by a physician.
Reported reactions include nausea, vomiting, fever, confusion, coma, renal failure, ileus, and leukopenia; death has been reported with extensive topical application, or application on mucous membranes. Interferon can be used; it is effective, but it is also expensive and its effect is inconsistent. Electrocauterization can be used; it is an older procedure but recovery time is generally longer. In severe cases of genital warts, treatment may require general or spinal anesthesia. This is a surgical procedure. More effective than cryosurgery and recurrence is at a much lower rate. Oral Isotretinoin is a therapy that has proven effective in experimental use, but is rarely used due to potentially severe side effects. In a small-scale study, low dose oral isotretinoin showed considerable efficacy and may represent an alternative systemic form of therapy for Genital Warts. Yet, albeit this indicative evidence not many studies have been conducted to further confirm the findings. In most countries this therapy is currently unapproved and only used as an alternative therapy if other therapies failed. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.16%3A_Viral_Diseases_of_the_Reproductive_System/15.16B%3A_Genital_Warts.txt |
Human immunodeficiency virus infection/acquired immunodeficiency syndrome is a disease of the human immune system caused by HIV.
Learning Objectives
• Describe the mode of transmission, mechanisms of infection, treatment options, and WHO and CDC classifications for the human immunodeficiency virus (HIV)
Key Points
• During the initial HIV infection a person may experience a brief period of influenza-like illness. This is typically followed by a prolonged period without symptoms.
• HIV is transmitted primarily via unprotected sexual intercourse (including anal and even oral sex), contaminated blood transfusions and hypodermic needles, and from mother to child during pregnancy, delivery, or breastfeeding.
• Abacavir, a nucleoside analog reverse transcriptase inhibitor (NARTI or NRTI) is used to treat HIV. Current HAART options are combinations (or “cocktails”) consisting of at least three medications belonging to at least two types, or “classes,” of antiretroviralagents.
Key Terms
• immunodeficiency: A depletion in the body’s natural immune system, or in some component of it.
• AIDS: an infectious disease, caused by HIV, that causes the gradual degeneration of the body’s immune system
Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/ AIDS ) is a disease of the human immune system caused by the human immunodeficiency virus (HIV ). During the initial infection a person may experience a brief period of influenza-like illness. This is typically followed by a prolonged period without symptoms. As the illness progresses it interferes more and more with the immune system, making people much more likely to get infections, including opportunistic infections, and tumors that do not usually affect people with working immune systems.
HIV is transmitted primarily via unprotected sexual intercourse (including anal and even oral sex), contaminated blood transfusions and hypodermic needles, and from mother to child during pregnancy, delivery, or breastfeeding. Some bodily fluids, such as saliva and tears, do not transmit HIV. Prevention of HIV infection, primarily through safe sex and needle-exchange programs, is a key strategy to control the spread of the disease. There is no cure or vaccine; however, antiretroviral treatment can slow the course of the disease and may lead to a near-normal life expectancy. While antiretroviral treatment reduces the risk of death and complications from the disease, these medications are expensive and may be associated with side effects.
Virology
HIV is the cause of the spectrum of disease known as HIV/AIDS. HIV is a retrovirus that primarily infects components of the human immune system such as CD4+ T cells, macrophages and dendritic cells. It directly and indirectly destroys CD4+ T cells.HIV is a member of the genus Lentivirus, part of the family of Retroviridae. Lentiviruses share many morphological and biological characteristics. Many species of mammals are infected by lentiviruses, which are characteristically responsible for long-duration illnesses with a long incubation period. Lentiviruses are transmitted as single-stranded, positive-sense, enveloped RNA viruses. Upon entry into the target cell, the viral RNA genome is converted (reverse transcribed) into double-stranded DNA by a virally encoded reverse transcriptase that is transported along with the viral genome in the virus particle. The resulting viral DNA is then imported into the cell nucleus and integrated into the cellular DNA by a virally encoded integrase and host co-factors. Once integrated, the virus may become latent, allowing the virus and its host cell to avoid detection by the immune system. Alternatively, the virus may betranscribed, producing new RNA genomes and viral proteins that are packaged and released from the cell as new virus particles that begin the replication cycle anew. Two types of HIV have been characterized: HIV-1 and HIV-2. HIV-1 is the virus that was originally discovered (and initially referred to also as LAV or HTLV-III). It is more virulent, more infective, and is the cause of the majority of HIV infections globally. The lower infectivity of HIV-2 as compared with HIV-1 implies that fewer people exposed to HIV-2 will be infected per exposure. Because of its relatively poor capacity for transmission, HIV-2 is largely confined to West Africa.
Classifications of HIV infection
Two main clinical staging systems are used to classify HIV and HIV-related disease for surveillance purposes: the WHO disease staging system for HIV infection and disease, and the CDC classification system for HIV infection. The CDC’s classification system is more frequently adopted in developed countries. Since the WHO’s staging system does not require laboratory tests, it is suited to the resource-restricted conditions encountered in developing countries, where it can also be used to help guide clinical management. Despite their differences, the two systems allow comparison for statistical purposes.
The World Health Organization first proposed a definition for AIDS in 1986. Since then, the WHO classification has been updated and expanded several times, with the most recent version being published in 2007. The WHO system uses the following categories:
Primary HIV infection: May be either asymptomatic or associated with acute retroviral syndrome.
Stage I: HIV infection is asymptomatic with a CD4+ T cell count (also known as CD4 count) greater than 500/uL. May include generalized lymph node enlargement.
Stage II: Mild symptoms which may include minor mucocutaneous manifestations and recurrent upper respiratory tract infections. A CD4 count of less than 500/uL.
Stage III: Advanced symptoms which may include unexplained chronic diarrhea for longer than a month, severe bacterial infections including tuberculosis of the lung as well as a CD4 count of less than 350/uL.
Stage IV or AIDS: severe symptoms which includes toxoplasmosis of the brain, candidiasis of the esophagus, trachea, bronchi or lungs and Kaposi’s sarcoma. A CD4 count of less than 200/uL.
The United States Center for Disease Control and Prevention also created a classification system for HIV, and updated it in 2008. In this system HIV infections are classified based on CD4 count and clinical symptoms, and describes the infection in three stages:
Stage 1: CD4 count ≥ 500 cells/uL and no AIDS defining conditions
Stage 2: CD4 count 200 to 500 cells/uL and no AIDS defining conditions
Stage 3: CD4 count ≤ 200 cells/uL or AIDS defining conditions
Unknown: if insufficient information is available to make any of the above classificationsFor surveillance purposes, the AIDS diagnosis still stands even if, after treatment, the CD4+ T cell count rises to above 200 per µL of blood or other AIDS-defining illnesses are cured.
Antiviral therapy
Abacavir, a nucleoside analog reverse transcriptase inhibitor (NARTI or NRTI) is used to treat HIV. Current HAART options are combinations (or “cocktails”) consisting of at least three medications belonging to at least two types, or “classes,” of antiretroviralagents. Initially treatment is typically a non-nucleoside reverse transcriptase inhibitor (NNRTI) plus two nucleoside analogue reverse transcriptase inhibitors(NRTIs). Typical NRTIs include: zidovudine (AZT) or tenofovir (TDF) and lamivudine (3TC) or emtricitabine (FTC). Combinations of agents which include a protease inhibitors (PI) are used if the above regime loses effectiveness. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.16%3A_Viral_Diseases_of_the_Reproductive_System/15.16C%3A_HIV_and_AIDS.txt |
Human papillomavirus (HPV) is a virus from the papillomavirus family that is capable of infecting humans.
Learning Objectives
• Discuss the relationship between the human papillomavirus (HPV) and the development of cancer
Key Points
• HPVs establish productive infections only in keratinocytes of the skin or mucous membranes.
• While the majority of the known types of HPV cause no symptoms in most people, some types can cause warts (verrucae), while others can – in a minority of cases – lead to cancers of the cervix, vulva, vagina, penis, oropharynx and anus.
• In more developed countries, cervical screening using a Papanicolaou (Pap) test or liquid-based cytology is used to detect abnormal cells that may develop into cancer. If abnormal cells are found, women are invited to have a colposcopy.
• HPV vaccines (Cervarix and Gardasil), which prevent infection with the HPV types (16 and 18) that cause 70% of cervical cancer, may lead to further decreases in cervical cancer.
Key Terms
• verrucae: warts
• Papanicolaou (Pap) test: screening of the cervical cells used to detect abnormal cells that may develop into cancer.
Human papillomavirus (HPV) is a virus from the papillomavirus family that is capable of infecting humans. Like all papillomaviruses, HPVs establish productive infections only in keratinocytes of the skin or mucous membranes. While the majority of the known types of HPV cause no symptoms in most people, some types can cause warts (verrucae), while others can – in a minority of cases – lead to cancers of the cervix, vulva, vagina, penis, oropharynx and anus. Recently, HPV has been linked with an increased risk of cardiovascular disease. In addition, HPV 16 and 18 infections are strongly associated with an increased odds ratio of developing oropharyngeal (throat) cancer.
More than 30 to 40 types of HPV are typically transmitted through sexual contact and infect the anogenital region. Some sexually transmitted HPV types may cause genital warts. Persistent infection with “high-risk” HPV types — different from the ones that cause skin warts — may progress to precancerous lesions and invasive cancer. HPV infection is a cause of nearly all cases of cervical cancer. However, most infections with these types do not cause disease.
Most HPV infections in young females are temporary and have little long-term significance. Seventy percent of infections are gone in 1 year and ninety percent in 2 years. However, when the infection persists — in 5% to 10% of infected women — there is high risk of developing precancerous lesions of the cervix, which can progress to invasive cervical cancer. This process usually takes 10–15 years, providing many opportunities for detection and treatment of the pre-cancerous lesion. Progression to invasive cancer can be almost always prevented when standard prevention strategies are applied, but the lesions still cause considerable burden necessitating preventive surgeries, which do in many cases involve loss of fertility.
In more developed countries, cervical screening using a Papanicolaou (Pap) test or liquid-based cytology is used to detect abnormal cells that may develop into cancer. If abnormal cells are found, women are invited to have a colposcopy. During a colposcopic inspection, biopsies can be taken and abnormal areas can be removed with a simple procedure, typically with a cauterizing loop or, more commonly in the developing world — by freezing (cryotherapy). Treating abnormal cells in this way can prevent them from developing into cervical cancer.
Pap smears have reduced the incidence and fatalities of cervical cancer in the developed world, but even so there were 11,000 cases and 3,900 deaths in the U.S. in 2008. Cervical cancer has substantial mortality in resource-poor areas; worldwide, there are an estimated 490,000 cases and 270,000 deaths each year.
HPV vaccines (Cervarix and Gardasil), which prevent infection with the HPV types (16 and 18) that cause 70% of cervical cancer, may lead to further decreases.
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Candidal vulvovaginitis is an infection of the vagina’s mucous membranes caused by Candida albicans.
Learning Objectives
• Analyze the symptoms and factors involved in vulvovaginal candidiasis
Key Points
• Up to 75% of women will have this infection at some point in their lives, and approximately 5% will have recurring episodes. It is the second most common cause of vaginal inflammation after bacterial vaginosis.
• The Candida species of fungus is found naturally in the vagina, and is usually harmless.
• It is not known exactly how changes in the vagina trigger thrush, but it may be due to a hormone (chemical) imbalance. In most cases, the cause of the hormonal changes is unknown. Some possible risk factors have been identified, such as taking antibiotics.
Key Terms
• Candida albicans: a diploid asexual fungus (a form of yeast). An overgrowth results in candidiasis in immunocompromised patients.
• vulvovaginal candidiasis: candidal vulvovaginitis or vaginal thrush is an infection of the vagina’s mucous membranes by Candida albicans.
Candidal vulvovaginitis or vaginal thrush is an infection of the vagina’s mucous membranes by Candida albicans. Up to 75% of women will have this infection at some point in their lives, and approximately 5% will have recurring episodes. It is the second most common cause of vaginal inflammation after bacterial vaginosis.
It is most commonly caused by a type of fungus known as Candida albicans. The Candida species of fungus is found naturally in the vagina, and is usually harmless. However, if the conditions in the vagina change, Candida albicans can cause the symptoms of thrush. Symptoms of thrush can also be caused by Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis. Non-albican Candida are commonly found in complicated cases of vaginal thrush such that first line treatment is ineffective. These cases are more likely in immunocompromised patients.
It is not known exactly how changes in the vagina trigger thrush, but it may be due to a hormone (chemical) imbalance. In most cases, the cause of the hormonal changes is unknown. Some possible risk factors have been identified, such as taking antibiotics.
The symptoms of vaginal thrush include vulval itching, vulval soreness and irritation, pain or discomfort during sexual intercourse (superficial dyspareunia), pain or discomfort during urination (dysuria) and vaginal discharge, which is usually odorless. The discharge can be thin and watery, or thick and white, like cottage cheese.
In addition to the above symptoms of thrush, vulvovaginal inflammation can also be present. The signs of vulvovaginal inflammation include erythema (redness) of the vagina and vulva, vagina fissuring (cracked skin), oedema (swelling from a build-up of fluid), also in severe cases, satellite lesions (sores in the surrounding area). This is rare, but may indicate the presence of another fungal condition, or the herpes simplex virus (the virus that causes genital herpes).
While vulvovaginal candidiasis is caused by a the yeast Candida there are many predisposing factors:
• Infection occurs in about 30% of women who are taking a course of oral antibiotics. The evidence of the effect of oral contraceptives is controversial.
• In pregnancy, changes in the levels of female sex hormones, such as estrogen, make a woman more likely to develop a yeast infection. During pregnancy, the Candida fungus is more prevalent (common), and recurrent infection is also more likely.
• Frequency of sexual intercourse appears to be related to the frequency of infections, however infections often occur without sex. Tight-fitting clothing, such as tights and thong underwear, do not appear to increase the risk. Neither do personal hygiene methods.
• Those with poorly controlled diabetes have increased rates of infection while those with well-controlled diabetes do not.
• The risk of developing thrush is also increased in a immunodeficiency, for example, by an immunosuppressive condition, such as HIV or AIDS, or receiving chemotherapy. This is because in these circumstances the body’s immune system, which usually fights off infection, is unable to effectively control the spread of the Candida fungus. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.17%3A_Fungal_and_Protozoan_Diseases_of_the_Reproductive_System/15.17A%3A_Vulvovaginal_Candidiasis.txt |
Trichomoniasis is primarily an infection of the urogenital tract; the most common site of infection is the urethra and the vagina in women.
Learning Objectives
• Outline the causes and symptoms associated with trichomoniasis
Key Points
• Trichomoniasis is a sexually transmitted disease, and is caused by the single-celled protozoan parasite Trichomonas vaginalis producing mechanical stress on host cells and then ingesting cell fragments after cell death.
• Symptoms usually appear in women within 5 to 28 days of exposure. In many cases, men may hold the parasite for some years without any signs (dormant).
• Trichomoniasis is diagnosed by visually observing the trichomonads via a microscope.
Key Terms
• trichomoniasis: A common sexually transmitted disease caused by the parasite Trichomonas vaginalis and infecting the urinary tract or vagina.
• vaginitis: Inflammation of the vagina.
• trichomonads: flagellate protozoa of the genus Trichomonas.
Trichomoniasis, sometimes referred to as “trich”, is a common cause of vaginitis. It is a sexually transmitted disease, and is caused by the single-celled protozoan parasite Trichomonas vaginalis producing mechanical stress on host cells and then ingesting cell fragments after cell deat. Trichomoniasis is primarily an infection of the urogenital tract; the most common site of infection is the urethra and the vagina in women. Typically, only women experience symptoms associated with Trichomonas infection.
Symptoms include inflammation of the cervix (cervicitis), urethra (urethritis), and vagina (vaginitis) which produces an itching or burning sensation. Discomfort may increase during intercourse and urination. There may also be a yellow-green, itchy, frothy, foul-smelling (“fishy” smell) vaginal discharge. In rare cases, lower abdominal pain can occur. Symptoms usually appear in women within 5 to 28 days of exposure. In many cases, men may hold the parasite for some years without any signs (dormant). Some sexual health specialists have stated that the condition can probably be carried in the vagina for years, despite standard tests being negative. While symptoms are most common in women, some men may temporarily exhibit symptoms such as an irritation inside the penis, mild discharge or slight burning after urination or ejaculation. Trichomoniasis is diagnosed by visually observing the trichomonads via a microscope. In women, the examiner collects the specimen during a pelvic examination by inserting a speculum into the vagina and then using a cotton-tipped applicator to collect the sample. The sample is then placed onto a microscopic slide and sent to a laboratory to be analyzed.
15.17C: The TORCH Panel of Tests
TORCH infections are a group of viral, bacterial, and protozoan infections that gain access to the fetal bloodstream from the mother.
Learning Objectives
• Summarize the importance of a TORCH panel of tests
Key Points
• The TORCH complex acronym spells out: T – Toxoplasmosis / Toxoplasma gondii; O – Other infections; R – Rubella; C – Cytomegalovirus; H – Herpes simplex virus.
• TORCH infections cause a syndrome characterized by microcephaly, sensorineural deafness, chorioretinitis, hepatosplenomegaly, and thrombocytopenia.
• Symptoms of a TORCH infection may include fever and difficulty feeding, with the newborn often small for their gestational age.
Key Terms
• haematogenous: Spread by blood.
• petechial: Characterised by, pertaining to, or resembling petechiae (small, nonraised haemorrhages on the skin).
• TORCH complex: TORCH complex is a medical acronym for a set of perinatal infections (which are infections that are passed from a pregnant woman to her fetus).
TORCH complex is a medical acronym for a set of perinatal infections (which are infections passed from a pregnant woman to her fetus). TORCH infections can lead to severe fetal anomalies or even fetal loss. They are a group of viral, bacterial, and protozoan infections that gain access to the fetal bloodstream through the placenta via the chorionic villi. Haematogenous transmission may occur at any time during gestation or occasionally at the time of delivery via maternal-to-fetal transfusion. The TORCH panel is used to screen for certain infectious diseases that can cause birth defects in a baby if the mother contracts them during the pregnancy. The TORCH panel of tests acronym spells out as follows:
• T – Toxoplasmosis / Toxoplasma gondii
• O – Other infections
• R – Rubella
• C – Cytomegalovirus
• H – Herpes simplex virus
The “other infections” included under the letter O include Coxsackievirus, Syphilis, Varicella-Zoster Virus, HIV, and Parvovirus B19. Hepatitis B is also sometimes included among “other infections,” but Hepatitis B is a large virus and does not cross the placenta, hence it cannot infect the fetus unless there have been breaks in the maternal-fetal barrier, such as can occur due to bleeding during childbirth or during amniocentesis.
TORCH infections cause a syndrome characterized by microcephaly, sensorineural deafness, chorioretinitis, hepatosplenomegaly, and thrombocytopenia. Symptoms of a TORCH infection may include fever and difficultly feeding. The newborn is often small for their gestational age. A petechial rash on the skin may be present, with small reddish or purplish spots due to bleeding from capillaries under the skin. An enlarged liver and spleen (hepatosplenomegaly) is common, as is jaundice. However, jaundice is less common in Hepatitis B because a newborn’s immune system is not developed well enough to mount a response against liver cells, as would normally be the cause of jaundice in an older child or adult. Hearing impairment, eye problems, mental retardation, autism, and death can be caused by TORCH infections. The TORCH panel is valuable for checking for infections because the mother often has a mild infection with few or no symptoms. It is also possible for genetic conditions (such as Aicardi-Goutieres syndrome) to present in a similar manner.
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The epidermis includes five main layers: the stratum corneum, stratum lucidium, stratum granulosum, stratum spinosum, and stratum germinativum.
LEARNING OBJECTIVES
Describe the layers of the epidermis
Key Points
• The epidermis provides a protective waterproof barrier that also keeps pathogens at bay and regulates body temperature.
• The main layers of the epidermis are: stratum corneum, stratum lucidium, stratum granulosm, stratum spinosum, stratum germinativum (also called stratum basale).
• Keratinocytes in the stratum basale proliferate during mitosis and the daughter cells move up the strata, changing shape and composition as they undergo multiple stages of cell differentiation.
Key Terms
• keratinocyte: the predominant cell type in the epidermis, the outermost layer of the skin, constituting 95% of the cells found there. Those keratinocytes found in the basal layer (stratum germinativum) of the skin are sometimes referred to as basal cells or basal keratinocytes.
• stratum germinativum: the basal layer—sometimes referred to as stratum basale—is the deepest of the five layers of the epidermis.
• stratum corneum: the most superficial layer of the epidermis from which dead skin sheds.
• epidermis: the outermost layer of skin.
• stratum lucidum: a layer of our skin that is found on the palms of our hands and the soles of our feet.
Layers of the Epidermis
The epidermis is the outermost layer of our skin. It is the layer we see with our eyes. It contains no blood supply of its own—which is why you can shave your skin and not cause any bleeding despite losing many cells in the process. Assuming, that is, you don’t nick your skin to deep, where the blood supply is actually found. The epidermis is itself divided into at least four separate parts. A fifth part is present in some areas of our body. In order from the deepest layer of the epidermis to the most superficial, these layers (strata) are the:
• Stratum basale
• Stratum spinosum
• Stratum granulosum
• Stratum lucidum
• Stratum corneum
Stratum Basale
The stratum basale, also called the stratum germinativum, is the basal (base) layer of the epidermis. It is the layer that’s closest to the blood supply lying underneath the epidermis.
This layer is one of the most important layers of our skin. This is because it contains the only cells of the epidermis that can divide via the process of mitosis, which means that skin cells germinate here, hence the word germinativum.
In this layer, the most numerous cells of the epidermis, called keratinocytes, arise thanks to mitosis. Keratinocytes produce the most important protein of the epidermis.
This protein is appropriately called keratin. Keratin makes our skin tough and provides us with much-needed protection from microorganisms, physical harm, and chemical irritation.
Millions of these new cells arise in the stratum basale on a daily basis. The newly produced cells push older cells into the upper layers of the epidermis with time. As these older cells move up toward the surface, they change their shape, nuclear, and chemical composition. These changes are, in part, what give the strata their unique characteristics.
Stratum Spinosum and Granulosum
From the stratum basale, the keratinocytes move into the stratum spinosum, a layer so called because its cells are spiny-shaped cells. The stratum spinosum is partly responsible for the skin’s strength and flexibility. From there the keratinocytes move into the next layer, called the stratum granulosum. This layer gets its name from the fact that the cells located here contain many granules. The keratinocytes produce a lot of keratin in this layer—they become filled with keratin. This process is known as keratinization. The keratinocytes become flatter, more brittle, and lose their nuclei in the stratum granulosum as well.
Stratum Lucidum
Once the keratinocytes leave the stratum granulosum, they die and help form the stratum lucidum. This death occurs largely as a result of the distance the keratinocytes find themselves from the rich blood supply the cells of the stratum basale lie on top off. Devoid of nutrients and oxygen, the keratinocytes die as they are pushed towards the surface of our skin. The stratum lucidum is a layer that derives its name from the lucid (clear/transparent) appearance it gives off under a microscope. This layer is only easily found in certain hairless parts of our body, namely the palms of our hands and the soles of our feet. Meaning, the places where our skin is usually the thickest.
Stratum Corneum
From the stratum lucidum, the keratinocytes enter the next layer, called the stratum corneum (the horny layer filled with cornified cells). This the only layer of skin we see with our eyes. The keratinocytes in this layer are called corneocytes. They are devoid of almost all of their water and they are completely devoid of a nucleus at this point. They are dead skin cells filled with the tough protein keratin. In essence, they are a protein mass more so than they are a cell. The corneocytes serve as a hard protective layer against environmental trauma, such as abrasions, light, heat, chemicals, and microorganism. The cells of the stratum corneum are also surrounded by lipids (fats) that help repel water as well. These corneocytes are eventually shed into the environment and become part of the dandruff in our hair or the dust around us, which dust mites readily munch on. This entire cycle, from new keratinocyte in the straum basale to a dead cell flaked off into the air, takes between 25–45 days.
Layers of the epidermis: The epidermis is made up of 95% keratinocytes but also contains melanocytes, Langerhans cells, Merkel cells, and inflammatory cells. The stratum basale is primarily made up of basal keratinocyte cells, which can be considered the stem cells of the epidermis. They divide to form the keratinocytes of the stratum spinosum, which migrate superficially. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.18%3A_Microbial_Diseases_of_the_Skin/15.18A%3A_Structure_of_the_Skin-_Epidermis.txt |
The skin flora, more properly referred to as the skin microbiome or skin microbiota, are the microorganisms that reside on the skin.
Learning Objectives
• Describe the types of skin flora and how they can be beneficial for the organism
Key Points
• Most bacteria on the skin are found in the superficial layers of the epidermis and the upper parts of hair follicles.
• Skin flora are usually non-pathogenic, and either commensals (are not harmful to their host) or mutualistic (offer a benefit).
• The benefits bacteria can offer include preventing transient pathogenic organisms from colonizing the skin surface, either by competing for nutrients, secreting chemicals against them, or stimulating the skin’s immune system.
• Resident microbes can cause skin diseases and enter the blood system creating life-threatening diseases particularly in immunosuppressed people.
Key Terms
• skin flora: the skin flora, more properly referred to as the skin microbiome or skin microbiota, are the microorganisms which reside on the skin.
• commensal: a term for a form of symbiosis in which one organism derives a benefit while the other is unaffected
• mutualistic: mutually beneficial.
The skin flora, more properly referred to as the skin microbiome or skin microbiota, are the microorganisms that reside on the skin. Most bacteria on the skin are found in the superficial layers of the epidermis and the upper parts of hair follicles. Skin flora are usually non-pathogenic, and either commensals (are not harmful to their host) or mutualistic (offer a benefit). The benefits bacteria can offer include preventing transient pathogenic organisms from colonizing the skin surface, either by competing for nutrients, secreting chemicals against them, or stimulating the skin’s immune system. However, resident microbes can cause skin diseases and enter the blood system creating life-threatening diseases particularly in immunosuppressed people. Hygiene to control such flora is important in preventing the transmission of antibiotic resistant hospital-acquired infections.
A major nonhuman skin flora is Batrachochytrium dendrobatidis, a chytrid and non-hyphal zoosporic fungus that causes chytridiomycosis, an infectious disease thought to be responsible for the decline in amphibian populations. The estimate of the number of species present on skin bacteria has been radically changed by the use of 16S ribosomal RNA to identify bacterial species present on skin samples direct from their genetic material. Previously such identification had depended upon microbiological culture upon which many varieties of bacteria did not grow and so were hidden to science. Staphylococcus epidermidis and Staphylococcus aureus were thought from cultural based research to be dominant. However, 16S ribosomal RNA research found that while common these species make up only 5% of skin bacteria. However, skin variety provides a rich and diverse habitat for bacteria. Most come from four phyla: Actinobacteria (51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%).
There are three main ecological areas for skin flora: sebaceous, moist, and dry. Propionibacteria and Staphylococci species are the main species in sebaceous areas. In moist places on the body Corynebacteria together with Staphylococci dominate. In dry areas, there is a mixture of species, but b-Proteobacteria and Flavobacteriales are dominant. Ecologically, sebaceous areas have greater species richness than moist and dry ones. The areas with least similarity between people in species are the spaces between fingers, the spaces between toes, axillae, and umbilical cord stump. Most similar are beside the nostril, nares (inside the nostril), and on the back.
Skin microflora can be commensals, mutualistic, or pathogens. Often they can be all three depending upon the strength of the person’s immune system. Research on the immune system in the gut and lungs has shown that microflora aids immunity development. However, such research has only started upon whether this is the case with the skin. Pseudomonas aeruginosa is an example of a mutualistic bacterium that can turn into a pathogen and cause disease. If it gains entry into the blood system it can result in infections in bone, joint, gastrointestinal, and respiratory systems and it can also cause dermatitis. However,
Pseudomonas aeruginosa produces antimicrobial substances such as pseudomonic acid (that are exploited commercially such as Mupirocin). This works against staphylococcal and streptococcal infections. Pseudomonas aeruginosa also produces substances that inhibit the growth of fungus species such as Candida krusei, Candida albicans, Torulopsis glabrata, Saccharomyces cerevisiae, and Aspergillus fumigatus. It can also inhibit the growth of Helicobacter pylori. Fatty acids (caproic acid) on the skin inhibit bacteria, especially after puberty, when undecylic acid becomes the primary fatty acid on the skin. Undecylic acid provides resistance to ringworm fungus and other skin infections.
Another aspect of bacteria is the generation of body odor. Sweat is odorless. However, several bacteria may consume it and create byproducts which may be considered putrid by man (as in contrast to flies, for example, that may find them attractive/appealing). For example, Propionibacteria in adolescent and adult produce propionic acid in sebaceous glands. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.18%3A_Microbial_Diseases_of_the_Skin/15.18B%3A_Microbiota_of_the_Skin.txt |
Bacterial skin infections include impetigo, erysipelas, and cellulitis.
LEARNING OBJECTIVES
Describe how impetigo, erysipelas and cellulitis are acquired and the treatment options available
Key Points
• Impetigo is a highly contagious bacterial skin infection most common among pre-school children primarily caused by Staphylococcus aureus and sometimes by Streptococcus pyogenes.
• Erysipelas is an acute streptococcus bacterial infection of the upper dermis and superficial lymphatics.
• Cellulitis is a diffuse inflammation of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin.
• Antimicrobial therapy is available for impetigo, erysipelas, and cellulitis.
Key Terms
• erysipelas: a severe skin disease caused by streptococcus infection in surface and surrounding tissue, marked by continued spreading inflammation
• impetigo: a contagious bacterial skin disease forming pustules and yellow crusty sores, chiefly on the face and hands. It is common in children. Infection is often through cuts or insect bites.
• cellulitis: an inflammation of subcutaneous or connective tissue caused by a bacterial infection
Common Bacterial Skin Infections
Bacterial skin infections include impetigo, erysipelas, and cellulitis.
IMPETIGO
Impetigo is a highly contagious bacterial skin infection most common among pre-school children. It is primarily caused by Staphylococcus aureus and sometimes by Streptococcus pyogenes. The infection is spread by direct contact with lesions or with nasal carriers. The incubation period is 1–3 days. Dried streptococci in the air are not infectious to intact skin. Scratching may spread the lesions. Impetigo generally appears as honey-colored scabs formed from dried serum and is often found on the arms, legs, or face . For generations, the disease was treated with an application of the antiseptic gentian violet. Today, topical or oral antibiotics are usually prescribed.
ERYSIPELAS
Erysipelas is an acute streptococcus bacterial infection of the upper dermis and superficial lymphatics. This disease is most common among the elderly, infants, and children. People with immune deficiency, diabetes, alcoholism, skin ulceration, fungal infections, and impaired lymphatic drainage (e.g., after mastectomy, pelvic surgery, bypass grafting) are also at increased risk. Patients typically develop symptoms including high fevers, shaking, chills, fatigue, headaches, vomiting, and general illness within 48 hours of the initial infection. The erythematous skin lesion enlarges rapidly and has a sharply demarcated raised edge. It appears as a red, swollen, warm, hardened and painful rash, similar in consistency to an orange peel. More severe infections can result in vesicles, bullae, and petechiae, with possible skin necrosis. Lymph nodes may be swollen and lymphedema may occur. Occasionally, a red streak extending to the lymph node can be seen. Most cases of erysipelas are due to Streptococcus pyogenes (also known as beta-hemolytic group A streptococci), although non-group A streptococci can also be the causative agent. Beta-hemolytic, non-group A streptococci include Streptococcus agalactiae, also known as group B strep or GBS. Depending on the severity, treatment involves either oral or intravenous antibiotics, using penicillins, clindamycin, or erythromycin. While illness symptoms resolve in a day or two, the skin may take weeks to return to normal.
CELLULITIS
Cellulitis is a diffuse inflammation of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken. Common points of infection include cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, intravenous drug injection, or sites of intravenous catheter insertion. Group A Streptococcus and Staphylococcus are the most common of these bacteria, which are part of the normal flora of the skin, but normally cause no actual infection while on the skin’s outer surface. Skin on the face or lower legs is most commonly affected by this infection, though cellulitis can occur on any part of the body. The mainstay of therapy remains treatment with appropriate antibiotics Recovery periods last from 48 hours to six months. The typical signature symptom of cellulitis is an area which is red, hot, and tender . Cellulitis is most often a clinical diagnosis, and local cultures do not always identify the causative organism. Blood cultures usually are positive only if the patient develops generalized sepsis.Treatment consists of resting the affected area, cutting away dead tissue, and administration of antibiotics (either oral or intravenous). | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.18%3A_Microbial_Diseases_of_the_Skin/15.18C%3A_Bacterial_Skin_Diseases.txt |
Virus-related cutaneous conditions include cold sores, shingles, and warts.
Learning Objectives
• Describe what causes cold sores, shingles and warts and the treatment options available
Key Points
• Oral herpes, the visible symptoms of which are colloquially called cold sores or fever blisters, is an infection of the face or mouth and is the most common form of infection by herpes simplex.
• Herpes zoster (or simply zoster), commonly known as shingles, is a viral disease caused by reactivation of latent varizella zoster virus and characterized by a painful skin rash with blisters in a limited area on one side of the body, often in a stripe.
• A wart is generally a small, rough growth, typically on a human’s hands or feet that can resemble a cauliflower or a solid blister and it is caused by infection by the human papilloma virus.
Key Terms
• shingles: a viral disease characterized by a painful skin rash with blisters in a limited area on one side of the body, often in a stripe
• wart: a type of deformed growth occurring on the skin caused by the human papillomavirus (HPV).
• cold sore: a small bump on the lips resulting from infection by the herpes virus.
• zoster: the disease called herpes zoster (from the typically beltlike pattern of its rash); shingles.
Virus-related cutaneous conditions are caused by two main groups of viruses–DNA and RNA types–both of which are obligatory intracellular parasites.
A cutaneous condition is any medical condition that affects the integumentary system — the organ system that comprises the entire surface of the body and includes skin, hair, nails, and related muscle and glands. Conditions of the human integumentary system constitute a broad spectrum of diseases, also known as dermatoses. While only a small number of skin diseases account for most visits to the physician, thousands of skin conditions have been described. Three common skin conditions that result from viral infections are cold sores, shingles, and warts.
Herpes
Herpes simplex is a viral disease from the herpesviridae family caused by both Herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2). Infection with the herpes virus is categorized into one of several distinct disorders based on the site of infection. Oral herpes , the visible symptoms of which are colloquially called cold sores or fever blisters, is an infection of the face or mouth and is the most common form of infection. Genital herpes, known simply as herpes, is the second most common form of herpes. Herpes simplex is most easily transmitted by direct contact with a lesion or the body fluid of an infected individual. Transmission may also occur through skin-to-skin contact during periods of asymptomatic shedding. Barrier protection methods are the most reliable method of preventing transmission of herpes, but they merely reduce rather than eliminate risk. Oral herpes is easily diagnosed if the patient presents with visible sores or ulcers. Once infected, the virus remains in the body for life. Recurrent infections (outbreaks) may occur from time to time, especially in times of immune impairment such as HIV and cancer-related immune suppression. However, after several years, outbreaks become less severe and more sporadic, and some people will become perpetually asymptomatic and will no longer experience outbreaks, though they may still be contagious to others. Treatments with antivirals can reduce viral shedding and alleviate the severity of symptomatic episodes.
Herpes Zoster
Herpes zoster (or simply zoster), commonly known as shingles, is a viral disease characterized by a painful skin rash with blisters in a limited area on one side of the body, often in a stripe. The initial infection with varicella zoster virus (VZV) causes the acute (short-lived) illness chickenpox which generally occurs in children and young people. Once an episode of chickenpox has resolved, the virus is not eliminated from the body but remains latent and can go on to cause shingles—an illness with very different symptoms—often many years after the initial infection. Although the zoster rash usually heals within two to four weeks, some sufferers experience residual nerve pain for months or years, a condition called postherpetic neuralgia. Exactly how the virus remains latent in the body, and subsequently re-activates is not understood. The earliest symptoms of herpes zoster, which include headache, fever, and malaise, are nonspecific, and may result in an incorrect diagnosis. In most cases after 1–2 days, but sometimes as long as three weeks, the initial phase is followed by the appearance of the characteristic skin rash. The pain and rash most commonly occurs on the torso, but can appear on the face, eyes, or other parts of the body.
At first the rash appears similar to the first appearance of hives. However, unlike hives, herpes zoster causes skin changes limited to a dermatome, normally resulting in a stripe or belt-like pattern that is limited to one side of the body and does not cross the midline. The goals of treatment are to limit the severity and duration of pain, shorten the duration of a shingles episode, and reduce complications. Symptomatic treatment is often needed for the complication of postherpetic neuralgia. Topical lotions containing calamine can be used on the rash or blisters and may be soothing. Antiviral drugs inhibit VZV replication and reduce the severity and duration of herpes zoster with minimal side effects, but do not reliably prevent postherpetic neuralgia. Of these drugs, acyclovir has been the standard treatment.
A wart is generally a small, rough growth, typically on a human’s hands or feet , but often other locations, that can resemble a cauliflower or a solid blister. They are caused by a viral infection, specifically by one of the many types of human papillomavirus (HPV). It is possible to get warts from others. They are contagious and usually enter the body in an area of broken skin. They typically disappear after a few months but can last for years and can recur. Gardasil is an HPV vaccine aimed at preventing cervical cancers and genital warts. There are many treatments and procedures associated with wart removal. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.18%3A_Microbial_Diseases_of_the_Skin/15.18D%3A_Viral_Skin_Diseases.txt |
Common fungal skin diseases include athlete’s foot, jock itch, and ringworm.
Learning Objectives
• Describe how fungal skin and nail diseases arise, their characteristic symptoms and the treatment options available
Key Points
• Athlete’s foot (also known as ringworm of the foot and tinea pedis) is an infection of the skin that causes scaling, flaking, and itching of affected areas and is caused by a fungi in the genus Trichophyton.
• Tinea cruris, also known as jock itch, is a dermatophyte fungal infection of the groin region in any sex, though more often seen in males.
• Dermatophytosis or ringworm is a clinical condition caused by fungal infection of the skin in humans, pets such as cats, and domesticated animals such as sheep and cattle.
Key Terms
• jock itch: a fungal infection, tinea cruris, of the groin region, due to the fungus Trichophyton rubrum and others.
• ringworm: a contagious fungal affliction of the skin, characterized by ring-shaped discoloured patches, covered by vesicles or scales.
• athlete’s foot: a fungal infection of the skin of the foot, usually between the toes, caused by the pathogen fungi. Scientific name: tinea pedis.
A cutaneous condition is any medical condition that affects the integumentary system — the organ system that comprises the entire surface of the body and includes skin, hair, nails, and related muscle and glands. Conditions of the human integumentary system constitute a broad spectrum of diseases, also known as dermatoses, as well as many nonpathologic states (like, in certain circumstances, melanonychia and racquet nails). Common fungal skin and nail diseases include athlete’s foot, jock itch, and ringworm.
Athlete’s foot (also known as ringworm of the foot and tinea pedis; ) is an infection of the skin that is caused by a fungi in the genus Trichophyton. While it is typically transmitted in moist communal areas where people walk barefoot, the disease requires a warm moist environment, such as the inside of a shoe, in order to incubate. Athlete’s foot causes scaling, flaking, and itching of the affected skin. Blisters and cracked skin may also occur, leading to exposed raw tissue, pain, swelling, and inflammation. Secondary bacterial infection can accompany the fungal infection, sometimes requiring a course of oral antibiotics. Athlete’s foot can usually be diagnosed by visual inspection of the skin, but where the diagnosis is in doubt direct microscopy of a potassium hydroxide preparation (known as a KOH test) may help rule out other possible causes, such as eczema or psoriasis. Without medication athlete’s foot resolves in 30–40% of cases and topical antifungal medication consistently produce much higher percentages of a cure. Conventional treatment typically involves daily or twice daily application of a topical medication in conjunction with hygiene measures outlined in the above section on prevention. Keeping feet dry and practicing good hygiene is crucial to preventing reinfection. Severe or prolonged fungal skin infections may require treatment with oral antifungal medication.
Tinea cruris, also known as crotch itch, crotch rot, Dhobie itch, eczema marginatum, gym itch, jock itch, jock rot, and ringworm of the groin is a dermatophyte fungal infection of the groin region in any sex, though more often seen in males. As the common name for this condition implies, it causes itching or a burning sensation in the groin area, thigh skin folds, or anus. It may involve the inner thighs and genital areas, as well as extending back to the perineum and perianal areas. Affected areas may appear red, tan, or brown, with flaking, rippling, peeling, or cracking skin. Opportunistic infections (infections that are caused by a diminished immune system) are frequent. Fungus from other parts of the body (commonly tinea pedis or ‘athlete’s foot’) can contribute to this itch. A warm, damp environment allowing the fungus to cultivate greatly contributes; especially with tight, sweaty, or rubbing clothing such as a jockstrap. Medical professionals suggest keeping the groin area clean and dry by drying off thoroughly after bathing and putting on dry clothing right away after swimming or perspiring. Other recommendations to prevent this infection are: not sharing clothing or towels with others, showering immediately after athletic activities, wearing loose cotton underwear, avoiding tight-fitting clothes, and using antifungal powders. Tinea cruris is best treated with topical antifungal medications of the allylamine or azole type.
Dermatophytosis or ringworm is a clinical condition caused by fungal infection of the skin in humans, pets such as cats, and domesticated animals such as sheep and cattle. The term “ringworm” is a misnomer, since the condition is caused by fungi of several different species and not by parasitic worms. The fungi that cause parasitic infection (dermatophytes) feed on keratin, the material found in the outer layer of skin, hair, and nails. These fungi thrive on skin that is warm and moist, but may also survive directly on the outsides of hair shafts or in their interiors. In pets, the fungus responsible for the disease survives in skin and on the outer surface of hairs. Advice often given to prevent this infection includes: avoiding sharing clothing, sports equipment, towels, or sheets and washing clothes in hot water with fungicidal soap after suspected exposure to ringworm. After being exposed to places where the potential of being infected is high, one should wash with an antibacterial and anti-fungal soap or one that contains tea tree oil, which contains terpinen-4-ol. Antifungal treatments include topical agents such as miconazole, terbinafine, clotrimazole, ketoconazole, or tolnaftate applied twice daily until symptoms resolve — usually within one or two weeks | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.18%3A_Microbial_Diseases_of_the_Skin/15.18E%3A_Fungal_Skin_and_Nail_Diseases.txt |
Learning Objectives
• Describe how the parasitic skin infections creeping eruption, lice and scabies arise and the treatment options available
A cutaneous condition is any medical condition that affects the integumentary system — the organ system that comprises the entire surface of the body and includes skin, hair, nails, and related muscle and glands. The major function of this system is as a barrier against the external environment. Conditions of the human integumentary system constitute a broad spectrum of diseases, also known as dermatoses, as well as many nonpathologic states (like, in certain circumstances, melanonychia and racquet nails). Common parasitic skin diseases include creeping eruption, lice, and scabies.
Cutaneous larva migrans (abbreviated CLM) is a skin disease in humans caused by the larvae of various nematode parasites of the hookworm family (Ancylostomatidae). The most common species that cayse this disease in the Americas is Ancylostoma braziliense. Colloquially called creeping eruption due to the way it looks, the disease is also somewhat ambiguously known as “ground itch” or (in some parts of the southern U.S.) “sandworms,” as the larvae like to live in sandy soil. Another vernacular name is plumber’s itch. The medical term CLM literally means “wandering larvae in the skin. ” These parasites are found in dog and cat feces and although they are able to infect the deeper tissues of these animals (through to the lungs and then the intestinal tract), in humans they are only able to penetrate the outer layers of the skin and thus create the typical wormlike burrows visible underneath the skin . The parasites apparently lack the collagenase enzymes required to penetrate through the basement membrane deeper into the skin. The infection causes a red, intense itching eruption. The itching can become very painful and if scratched may allow a secondary bacterial infection to develop but it will stop after the parasites are dead. Systemic (oral) agents to treat this infection include albendazole (trade name Albenza) and ivermectin (trade name Stromectol).
Louse (plural: lice) is the common name for members of over 3,000 species of wingless insects of the order Phthiraptera, three of which are classified as human disease agents. They are obligate ectoparasites of every avian and mammalian order except for monotremes (the platypus and echidnas), bats, whales, dolphins, porpoises, and pangolins. Most lice are scavengers, feeding on skin and other debris found on the host’s body, but some species feed on sebaceous secretions and blood. Most are found only on specific types of animals, and, in some cases, only to a particular part of the body. Some animals are known to host up to 15 different species, although one to three is typical for mammals, and two to six for birds. For example, in humans, different species of louse inhabit the scalp and pubic hair. Lice generally cannot survive for long if removed from their host. Humans host three different kinds of lice: head lice, body lice, and pubic lice. Lice infestations can be controlled with lice combs and medicated shampoos or washes.
Scabies (from Latin: scabere, “to scratch”), known colloquially as the seven-year itch, is a contagious skin infection that occurs among humans and other animals. The disease may be transmitted from objects, but is most often transmitted by direct skin-to-skin contact, with a higher risk with prolonged contact. Initial infections require four to six weeks to become symptomatic. Reinfection, however, may manifest symptoms within as little as 24 hours. Because the symptoms are allergic, their delay in onset is often mirrored by a significant delay in relief after the parasites have been eradicated. The characteristic symptoms of a scabies infection include intense itching and superficial burrows . The burrow tracks are often linear, to the point that a neat “line” of four or more closely placed and equally developed mosquito-like “bites” is almost diagnostic of the disease. Scabies may be diagnosed clinically in geographical areas where it is common when diffuse itching presents along with either lesions in two typical spots or there is itchiness of another household member. The classical sign of scabies is the burrows made by the mites within the skin. To detect the burrow, the suspected area is rubbed with ink from a fountain pen or a topical tetracycline solution, which glows under a special light. A number of medications are effective in treating scabies with permethrin being the most effective treatment. However, treatment must often involve the entire household or community to prevent re-infection. Options to improve itchiness include antihistamines.
Key Points
• Cutaneous larva migrans is a skin disease in humans caused by the larvae of various nematode parasites of the hookworm family (Ancylostomatidae) and characterized by a red, intense itching eruption.
• Humans host three different kinds of lice (head lice, body lice, and pubic lice). Lice infestations can be controlled with lice combs and medicated shampoos or washes.
• Scabies, known colloquially as the seven-year itch, is a contagious skin infection that occurs among humans and other animals.
Key Terms
• scabies: an infestation of parasitic mites, Sarcoptes scabiei, causing intense itching caused by the mites burrowing into the skin of humans and other animals. It is easily transmissible from human to human; secondary skin infection may occur.
• cutaneous larva migrans: a skin disease in humans, caused by the larvae of various nematode parasites of the hookworm family (Ancylostomatidae).
• louse: a small parasitic wingless insect of the order Phthiraptera.
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Many structures in the human eye, such as the cornea and fovea, process light so it can be deciphered by rods and cones in the retina.
Learning Objectives
• Explain how eyes have evolved to benefit organisms
Key Points
• The cornea and the lens bend light to focus the image on the retina; the iris and pupil regulate the amount of light entering the eye.
• The aqueous humour maintains the convex shape of the cornea; the vitreous humour supports the lens and maintains the shape of the entire eye.
• Presbyopia occurs because the image focuses behind the retina; it is similar to hyperopia (farsightedness), which is caused by an eyeball that is too short.
• Myopia (nearsightedness) occurs when an eyeball is elongated; images in the distance appear blurry, but images nearby are clear.
• Rods are used for peripheral and nighttime vision; cones are used for daytime and color vision.
• The fovea is responsible for acute vision because it has a high density of cones.
Key Terms
• rod: a rod-shaped cell located in the outer retina of the eye that is extremely sensitive to light
• retina: the thin layer of cells at the back of the eyeball where light is converted into neural signals sent to the brain
• cone: cell located near the center of the retina that is weakly photosensitive and is responsible for color vision in relatively bright light
Anatomy of the Eye
The retina, a thin layer of cells located on the inner surface of the back of the eye, consists of photoreceptive cells, which are responsible for the transduction of light into nervous impulses. However, light does not enter the retina unaltered; it must first pass through other layers that process it so that it can be interpreted by the retina.
The cornea, the front transparent layer of the eye, along with the crystalline lens, refract (bend) light to focus the image on the retina. After passing through the cornea, light passes through the aqueous humour, which connects the cornea to the lens. This clear gelatinous mass also provides the corneal epithelium with nutrients and helps maintain the convex shape of the cornea. The iris, which is visible as the colored part of the eye, is a circular muscular ring lying between the lens and the aqueous humour that regulates the amount of light entering the eye. Light passes through the center of the iris, the pupil, which actively adjusts its size to maintain a constant level of light entering the eye. In conditions of high ambient light, the iris contracts, reducing the size of the pupil. In conditions of low light, the iris relaxes and the pupil enlarges.
The main function of the lens is to focus light on the retina and fovea centralis. The lens is a transparent, convex structure located behind the cornea. On the other side of the lens is the vitreous humour, which lets light through without refraction, maintains the shape of the eye, and suspends the delicate lens. The lens focuses and re-focuses light as the eye rests on near and far objects in the visual field. The lens is operated by muscles that stretch it flat or allow it to thicken, changing the focal length of light coming through to focus it sharply on the retina. With age comes the loss of the flexibility of the lens; a form of farsightedness called presbyopia results. Presbyopia occurs because the image focuses behind the retina. It is a deficit similar to a different type of farsightedness, hyperopia, caused by an eyeball that is too short. For both defects, images in the distance are clear, but images nearby are blurry. Myopia (nearsightedness) occurs when an eyeball is elongated and the image focus falls in front of the retina. In this case, images in the distance are blurry, but images nearby are clear.
There are two types of photoreceptors in the retina: rods and cones. Both are named for their general appearance. Rods, strongly photosensitive, are located in the outer edges of the retina. They detect dim light and are used primarily for peripheral and nighttime vision. Cones, weakly photosensitive, are located near the center of the retina. They respond to bright light; their primary role is in daytime, color vision.
The fovea is the region in the center back of the eye that is responsible for acute (central) vision. The fovea has a high density of cones. When you bring your gaze to an object to examine it intently in bright light, the eyes orient so that the object’s image falls on the fovea. However, when looking at a star in the night sky or other object in dim light, the object can be better viewed by the peripheral vision because it is the rods at the edges of the retina, rather than the cones at the center, that operate better in low light. In humans, cones far outnumber rods in the fovea. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.19%3A_Microbial_Diseases_of_the_Eye/15.19A%3A_Anatomy_of_the_Eye.txt |
A small number of bacteria are normally present in the conjunctiva.
Learning Objectives
• Give examples of the microorganisms found in the normal eye microbiota
Key Points
• The lachrymal glands continuously secrete tears keeping the conjunctiva moist, while intermittent blinking lubricates the conjunctiva and washes away foreign material.
• Tears contain bactericides such as lysozyme, so that microorganisms have difficulty in surviving the lysozyme and settling on the epithelial surfaces.
• Some pathogens able to infect the conjunctiva, such as Neisseria gonorrhoeae and Chlamydia trachomatis are thought to have special processes allowing them to attach to the conjunctival epithelium.
Key Terms
• lachrymal gland: The lacrimal glands are paired almond-shaped glands, one for each eye, that secrete the aqueous layer of the tear film.
• conjunctiva: A clear mucous membrane that lines the inner surface of the eyelid and the exposed surface of the eyeball or sclera.
• lysozyme: A bacteriolytic (or antibiotic) enzyme found in many animal secretions and in egg white.
Normal Eye Microbiota
The human microbiome (or human microbiota) is the aggregate of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. They include bacteria, fungi, and archaea. Some of these organisms perform tasks that are useful for the human host. However, the majority have been too poorly researched to understand the role they play. Those that are expected to be present and do not cause disease (under normal circumstances), but instead participate in maintaining health, are deemed members of the normal flora.
A small number of bacteria are normally present in the conjunctiva. These include: Chlamydia trachomatis, Chlamydophila pneumoniae, Haemophilus aegyptius, Haemophilus influenzae, Moraxella spp, Neisseria spp, Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus viridians. Staphylococcus epidermidis and certain coryneforms such as Propionibacterium acnes are dominant. Staphylococcus aureus, streptococci, Haemophilus sp. and Neisseria sp. sometimes occur. The lachrymal glands continuously secrete tears keeping the conjunctiva moist, while intermittent blinking lubricates the conjunctiva and washes away foreign material. Tears contain bactericides such as lysozyme, so that microorganisms have difficulty in surviving the lysozyme and settling on the epithelial surfaces.
Some pathogens able to infect the conjunctiva, such as Neisseria gonorrhoeae and Chlamydia trachomatis, are thought to have special processes allowing them to attach to the conjunctival epithelium. Newborn infants are particularly prone to bacterial attachment. Chlamydia and Neisseria may be present in an infected mother and show up on the cervical and vaginal epithelium. In such cases the newborn’s eyes may be treated with silver nitrate or antibiotics.
15.19C: Bacterial Eye Diseases
Conjunctivitis is inflammation of the conjunctiva, most commonly due to an infection.
LEARNING OBJECTIVES
Describe the various causes of conjunctivitis and keratitis and its symptoms
Key Points
• Classification can be either by extent of the inflamed area or by cause (allergic, bacterial, viral, or chemical).
• Red eye (hyperaemia), irritation (chemosis) and watering (epiphora) of the eyes are symptoms common to all forms of conjunctivitis.
• Keratitis, a condition in which the eye’s cornea becomes inflamed, is often marked by moderate to intense pain and usually involves impaired eyesight.
Key Terms
• conjunctivitis: An inflammation of the conjunctiva often due to infection.
• keratitis: Inflammation of the cornea.
Common Eye Infections
CONJUNCTIVITIS
Conjunctivitis, also called pink eye or Madras eye, is inflammation of the conjunctiva, which consists of the outermost layer of the eye and the inner surface of the eyelids. Conjunctivitis most commonly caused by a viral infection or, less commonly, a bacterial infection, or by an allergic reaction. Classification can be either by extent of the inflamed area or by cause (allergic, bacterial, viral or chemical). Neonatal conjunctivitis is often defined separately due to different organisms.
Symptoms and Diagnosis
An inflamed, red eye (hyperaemia), irritation (chemosis), and watering (epiphora) of the eyes are symptoms common to all forms of conjunctivitis. However, the pupils should be normally reactive and the visual acuity normal. Bacterial conjunctivitis due to common pyogenic (pus-producing) bacteria causes marked grittiness/irritation and a stringy, opaque, greyish or yellowish mucopurulent discharge that may cause the lids to stick together, especially after sleep. Another symptom that could be caused by bacterial conjunctivitis is severe crusting of the infected eye and the surrounding skin.
Contrary to popular belief, discharge is not essential to the diagnosis. Bacteria such as Chlamydia trachomatis or Moraxella can cause a non-exudative but persistent conjunctivitis without much redness. The gritty and/or scratchy feeling is sometimes localized enough for patients to insist they must have a foreign body in the eye. The more acute pyogenic infections can be painful. Like viral conjunctivitis, it usually affects only one eye but may spread easily to the other eye.
Corynebacterium diphtheriae causes membrane formation in conjunctiva of non immunized children. Bacterial conjunctivitis usually resolves without treatment. Antibiotics, eye drops, or ointment may only be needed if no improvement is observed after three days.
Chlamydiaconjunctivitis or trachoma was once the most important cause of blindness worldwide. The infection can be spread from eye to eye by fingers, shared towels or cloths, coughing and sneezing, and by eye-seeking flies. Newborns can also develop chlamydia eye infection through childbirth. Chlamydia can affect infants by causing spontaneous abortion, premature birth, and conjunctivitis, which may lead to blindness and pneumonia. Conjunctivitis due to chlamydia typically occurs one week after birth (compared with chemical causes (within hours) or gonorrhea (2–5 days)).
KERATITIS
Keratitis is a condition in which the eye’s cornea, the front part of the eye, becomes inflamed. The condition is often marked by moderate to intense pain and usually involves impaired eyesight. Superficial keratitis involves the superficial layers (i.e. the epithelium) of the cornea. After healing, this form of keratitis does not generally leave a scar. Deep keratitis involves deeper layers of the cornea (i.e. the epithelium, Bowman’s membrane and often stroma), and the natural course leaves a scar upon healing that impairs vision if it occurs on or near the visual axis. This can be reduced or avoided with the use of topical corticosteroid eyedrops.
Causes and Treatment
Keratitis has multiple causes. Bacterial infection of the cornea can follow from an injury or from result from wearing contact lenses. The bacteria involved are Staphylococcus aureus and, for contact lens wearers, Pseudomonas aeruginosa. Pseudomonas aeruginosa contains enzymes that can digest the cornea. Treatment depends on the cause of the keratitis. Infectious keratitis can progress rapidly, and generally requires urgent antibacterial, antifungal, or antiviral therapy to eliminate the pathogen. Treatment is usually carried out by an ophthalmologist and can involve prescription eye medications, systemic medication, or even intravenous therapy. It is inadvisable to use over-the-counter eye drops as they are typically not helpful in treating infections; using them could also delay crucial correct treatment, increasing the likelihood of sight-threatening complications. In addition, contact lens wearers are typically advised to discontinue contact lens wear and replace contaminated contact lenses and contact lens cases. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.19%3A_Microbial_Diseases_of_the_Eye/15.19B%3A_Normal_Eye_Microbiota.txt |
Fungi and viruses such as herpes simplex can cause eye infections.
LEARNING OBJECTIVES
Summarize the various types of herpes simplex keratitis: dendritic ulcer (epithelial keratitis) and disciform keratitis (stromal keratitis)
Key Points
• Improper hygiene is a major cause of fungal contamination of contact lenses.
• Herpetic simplex keratitis is a form of keratitis caused by recurrent herpes simplex virus in cornea.
• Primary infection most commonly manifests as blepharoconjunctivitis i.e. infection of lids and conjunctiva that heals without scarring.
Key Terms
• ulcer: An open sore of the skin, eyes, or mucous membrane, often caused by an initial abrasion and generally maintained by an inflammation and/or an infection.
• keratitis: Inflammation of the cornea.
• conjunctivitis: An inflammation of the conjunctiva often due to infection.
Microbial corneal infection is the most serious and “most common vision threatening” complication of wearing contact lenses, which is believed to be strongly associated with contact lens cases. Such infections “are being increasingly recognized as an important cause of morbidity and blindness” and “may even be life-threatening. ” While the cornea is believed to be the most common site for fungal eye infections, other parts of the eye such as the orbit, sclera, and eyelids may also be involved.
Fungal Infections of the Eye
Factors that contribute to fungal contamination of contact lenses include, but not limited to, hygiene negligence such as: improper sterilization and disinfection of contact lenses, use of contaminated lenses, contaminated contact lens case, contaminated contact lens solution, wearing of contact lenses during eye infections and introduction of micro-organisms from the environment.
Diagnosis is determined”by recognition of typical clinical features and through direct microscopic detection of fungi in scrapes, biopsy specimens, and other samples. “Ultimately, cultures that are made from the samples isolated from patients is what “confirms diagnosis. ” Other tests that may also be used if needed include “histopathological, immunohistochemical, or DNA -based tests. Pathogenesis of the fungal contaminants includes a wide range of factors such as invasiveness, toxigenicity, and host factors. Once diagnosis is accessed, specific anti-fungal therapy can be administered. One of the most popular and common treatments used”for life-threatening and severe ophthalmic mycoses is amphotericin B which is a specific anti-fungal drug. For the treatment for filamentous fungal keratitis, “topical natamycin is usually the first choice. For the treatment of yeast keratitis, topical amphotericin B is usually the first choice. Current advances in further treatments include evaluations of triazoles such as itraconazole and fluconazole” as therapeutic options in ophthalmic mycoses.
Viral Infections of the Eye
Herpes Simplex Virus
Herpetic simplex keratitis is a form of keratitis caused by recurrent herpes simplex virus in cornea. Herpes simplex virus (HSV) infection is very common in humans. HSV is a double-stranded DNA virus that has icosahedral capsid. HSV-1 infections are found more commonly in the oral area and HSV-2 in the genital area. Primary infection most commonly manifests as blepharoconjunctivitis i.e. infection of lids and conjunctiva that heals without scarring. Lid vesicles and conjunctivitis are seen in primary infection. Corneal involvement is rarely seen in primary infection. Recurrent herpes of the eye in turn is caused by reactivation of the virus in a latently infected sensory ganglion, transport of the virus down the nerve axon to sensory nerve endings, and subsequent infection of ocular surface. The following classification of herpes simplex keratitis is important for understanding this disease:
Dendritic Ulcer (Epithelial Keratitis)
This classic herpetic lesion consists of a linear branching corneal ulcer (dendritic ulcer). During eye exam the defect is examined after staining with fluorescein dye. The underlying corneal has minimal inflammation. Patients with epithelial keratitis complain of foreign-body sensation, light sensitivity, redness, and blurred vision. Focal or diffuse reduction in corneal sensation develops following recurrent epithelial keratitis. In immune deficient patients or with the use of corticosteroids the ulcer may become large and in these cases it is called geographic ulcer.
Disciform Keratitis (Stromal Kieratitis)
Stromal keratitis manifests as a disc-shaped area of corneal edema. Longstanding corneal edema leads to permanent scarring. It is the major cause of decreased vision associated with HSV. Localized endotheliis (localized inflammation of corneal endothelial layer) is the cause of disciform keratitis.
Diagnostic testing is seldom needed because of its classic clinical features and is not useful in stromal keratitis as there is usually no live virus. Laboratory tests are indicated in complicated cases when the clinical diagnosis is uncertain and in all cases of suspected neonatal herpes infection. Corneal smears or impression cytology specimens can be analyzed by culture, antigen detection, or fluorescent antibody testing. Demonstration of HSV is possible with viral culture. Serologic tests in turn may show a rising antibody titer during primary infection but are of no diagnostic assistance during recurrent episodes.
Treatment of herpes of the eye is different based on its presentation. Epithelial keratitis is caused by live virus. Stromal disease is an immune response. Metaherpetic ulcer results from inability of the corneal epithelium to heal. Epithelial keratitis is treated with topical antivirals, which are very effective with low incidence of resistance. Acyclovir ophthalmic ointment and Trifluridine eye drops have similar effectiveness but are more effective than Idoxuridine and Vidarabine eye drops. Topical antiviral medications are not absorbed by the cornea through an intact epithelium, but orally administered acyclovir penetrates an intact cornea and anterior chamber.
Cytomegalovirus Retinitis
Cytomegalovirus retinitis, also known as CMV retinitis, is an inflammation of the retina of the eye that can lead to blindness. Caused by human cytomegalovirus, it occurs predominantly in people whose immune system has been compromised.
Acanthamoeba
Acanthamoeba is a microscopic, free-living ameba (single-celled living organism) commonly found in the environment that can cause rare, but severe, eye illness. Acanthamoeba causes three main types of illness involving the eye (Acanthamoeba keratitis), the brain and spinal cord (Granulomatous Encephalitis), and infections that can spread throughout the entire body (disseminated infection).
Toxoplasma gondii
A single-celled parasite called Toxoplasma gondii causes a disease known as toxoplasmosis. While the parasite is found throughout the world, more than 60 million people in the United States may be infected with the Toxoplasma parasite. Of those who are infected, very few have symptoms because a healthy person’s immune system usually keeps the parasite from causing illness.
Signs and symptoms of ocular toxoplasmosis can include reduced vision, blurred vision, pain (often with bright light), redness of the eye, and sometimes tearing. Ophthalmologists sometimes prescribe medicine to treat active disease. Whether or not medication is recommended depends on the size of the eye lesion, the location, and the characteristics of the lesion (acute active, versus chronic not progressing). An ophthalmologist will provide the best care for ocular toxoplasmosis.
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The primary function of the nervous system is to coordinate and control the various body functions.
Learning Objectives
• Describe the functions of the nervous system
Key Points
• The nervous system is a highly integrated system. The nervous system has three overlapping functions based on sensory input, integration, and motor output.
• At a more integrative level, the primary function of the nervous system is to control and communicate information throughout the body.
Key Terms
• hormone: A molecule released by a cell or a gland in one part of the body that sends out messages affecting cells in other parts of the organism.
• nervous system: The organ system that coordinates the activities of muscles, monitors organs, constructs and processes data received from the senses, and initiates actions.
The nervous system has three overlapping functions based on the sensory input, integration, and motor output. The nervous system is a highly integrated system.
Sensory Input
Sensory input comes from the many sensory receptors that monitor changes occurring both inside and outside the body. The total sum of the information gathered by these receptors is called sensory input. The nervous system processes and interprets sensory input and decides what actions should be taken. The nervous system activates effector organs such as muscles and glands to cause a response called motor output.
Integration
At a more integrative level, the primary function of the nervous system is to control and communicate information throughout the body. It does this by extracting information from the environment using sensory receptors. This sensory input is sent to the central nervous system, which determines an appropriate response.
Motor Response
Once the response is activated, the nervous system sends signals via motor output to muscles or glands to initiate the response.
In humans, the sophistication of the nervous system allows for language, abstract representation of concepts, transmission of culture, and many other features of society that would not otherwise exist.
15.20B: Subdivisions of the Nervous System
The CNS includes the brain and spinal cord, while the PNS is a network of nerves linking the body to the brain and spinal cord.
Learning Objectives
• Describe the subdivisions of the nervous system
Key Points
• The nervous system is often divided into components called gray matter and white matter. Gray matter contains a relatively high proportion of neuron cell bodies and white matter is composed mainly of axons.
• The peripheral nervous system is subdivided into nerves, the autonomic system, and the somatic system. The autonomic nervous system is further subdivided into the parasympathetic and sympathetic nervous systems.
• The enteric nervous system is an independent subsystem of the peripheral nervous system.
• The central nervous system includes the brain and spinal cord and has various centers that integrate of all the information in the body. These can be subdivided into lower centers that carry out essential body functions and higher centers that control more sophisticated information processing.
Key Terms
• gray matter: A major component of the central nervous system, consisting of neuronal cell bodies, neuropil (dendrites and unmyelinated axons), glial cells (astroglia and oligodendrocytes), and capillaries.
• central nervous system: In vertebrates, the part of the nervous system comprising the brain, brainstem, and spinal cord.
• white matter: A region of the central nervous system containing myelinated nerve fibers and no dendrites.
• peripheral nervous system: This system consists of the nerves and ganglia outside of the brain and spinal cord.
The nervous system is comprised of two major subdivisions, the central nervous system (CNS) and the peripheral nervous system (PNS).
Central Nervous System
The CNS includes the brain and spinal cord along with various centers that integrate all the sensory and motor information in the body. These centers can be broadly subdivided into lower centers, including the spinal cord and brain stem, that carry out essential body and organ-control functions and higher centers within the brain that control more sophisticated information processing, including our thoughts and perceptions. Further subdivisions of the brain will be discussed in a later section.
Gray Matter and White Matter
The nervous system is often divided into components called gray matter and white matter. Gray matter, which is gray in preserved tissue but pink or light brown in living tissue, contains a relatively high proportion of neuron cell bodies. Conversely, white matter is composed mainly of axons and is named because of the color of the fatty insulation called myelin that coats many axons. White matter includes all of the nerves of the PNS and much of the interior of the brain and spinal cord. Gray matter is found in clusters of neurons in the brain and spinal cord and in cortical layers that line their surfaces.
By convention, a cluster of neuron cell bodies in the gray matter of the brain or spinal cord is called a nucleus, whereas a cluster of neuron cell bodies in the periphery is called a ganglion. However, there are a few notable exceptions to this rule, including a part of the brain called the basal ganglia, which will be discussed later.
Peripheral Nervous System
The PNS is a vast network of nerves consisting of bundles of axons that link the body to the brain and the spinal cord. Sensory nerves of the PNS contain sensory receptors that detect changes in the internal and external environment. This information is sent to the CNS via afferent sensory nerves. Following information processing in the CNS, signals are relayed back to the PNS by way of efferent peripheral nerves.
Autonomic and Somatic Nervous Systems
The PNS is further subdivided into the autonomic nervous system (ANS) and the somatic nervous system. The autonomic system has involuntary control of internal organs, blood vessels, and smooth and cardiac muscles. The somatic system has voluntary control of our movements via skeletal muscle.
As mentioned, the autonomic nervous system acts as a control system and most functions occur without conscious thought. The ANS affects heart rate, digestion, respiratory rate, salivation, perspiration, pupil diameter, urination, and sexual arousal. While most of its actions are involuntary, some, such as breathing, work in tandem with the conscious mind. The ANS is classically divided into two subsystems: the parasympathetic nervous system (PSNS) and sympathetic nervous system (SNS).
Parasympathetic and Sympathetic Nervous Systems
Broadly, the parasympathetic system is responsible for stimulation of “rest-and-digest” activities that occur when the body is at rest, including sexual arousal, salivation, lacrimation (tears), urination, digestion, and defecation. The sympathetic nervous syste is responsible for stimulating activities associated with the “fight-or-flight” response: mobilizing the systems of the body for escape or attacking sources of danger. In truth, the functions of both the parasympathetic and sympathetic nervous systems are not so straightforward, but this division is a useful rule of thumb.
The enteric nervous system (ENS) controls the gastrointestinal system and is sometimes considered part of the autonomic nervous system. However, it is sometimes considered an independent system because it can operate independently of the brain and the spinal cord. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20A%3A_Functions_of_the_Nervous_System.txt |
Learning Objectives
• Discuss the various causes (viral, bacteria, fungi and protozoa) and modes of transmission for meningitis
Meningitis is inflammation of the protective membranes covering the brain and spinal cord, known collectively as the meninges. The inflammation may be caused by infection with viruses, bacteria, or other microorganisms, and less commonly by certain drugs. Meningitis can be life-threatening because of the inflammation’s proximity to the brain and spinal cord. Therefore, the condition is classified as a medical emergency.
The most common symptoms of meningitis are headache and neck stiffness associated with fever, confusion or altered consciousness, vomiting, and an inability to tolerate light (photophobia) or loud noises (phonophobia). Children often exhibit only nonspecific symptoms, such as irritability and drowsiness. If a rash is present, it may indicate a particular cause of meningitis. For instance, meningitis caused by the bacterium Neisseria meningitidis (known as “meningococcal menigitis”) can be differentiated from meningitis with other causes by a rapidly spreading petechial rash, which may precede other symptoms. The rash consists of numerous small, irregular purple or red spots (“petechiae”) on the trunk, lower extremities, mucous membranes, conjuctiva, and (occasionally) the palms of the hands or soles of the feet. Meningococcal bacteria may be accompanied by a characteristic rash. Seizures may also occur for various reasons. In children, seizures are common in the early stages of meningitis and do not necessarily indicate an underlying cause.
Meningitis can lead to serious long-term consequences such as deafness, epilepsy, hydrocephalus, and cognitive deficits, especially if not treated quickly. Some forms of meningitis (such as those associated with meningococci, Haemophilus influenzae type B, pneumococci, or mumps virus infections) may be prevented by immunization.
Meningitis is typically caused by an infection with microorganisms. Most infections are due to viruses (such as enteroviruses or herpes simplex virus), with bacteria (for example group B streptococci), fungi, and protozoa being the next most common causes. It may also result from various non-infectious causes. The term aseptic meningitis refers to cases of meningitis in which no bacterial infection can be demonstrated. This type of meningitis is usually caused by viruses, but it may be due to bacterial infection that has already been partially treated, when bacteria disappear from the meninges, or pathogens infect a space adjacent to the meninges (e.g. sinusitis). Endocarditis (an infection of the heart valves which spreads small clusters of bacteria through the bloodstream) may cause aseptic meningitis. Aseptic meningitis may also result from infection with spirochetes, a type of bacteria that includes Treponema pallidum (the cause of syphilis) and Borrelia burgdorferi (known for causing Lyme disease).
A lumbar puncture diagnoses or excludes meningitis. A needle is inserted into the spinal canal to extract a sample of cerebrospinal fluid (CSF) which envelops the brain and spinal cord. The CSF is examined in a medical laboratory. In someone suspected of having meningitis, blood tests are performed for markers of inflammation (e.g. C-reactive protein, complete blood count) as well as blood cultures.
The first treatment in acute meningitis consists of antimicrobial and sometimes antiviral therapy. In addition, corticosteroids can also be used to prevent complications from excessive inflammation. The introduction of pneumococcal vaccine has lowered rates of pneumococcal meningitis in both children and adults. Recent skull trauma potentially allows nasal cavity bacteria to enter the meningeal space. Similarly, devices in the brain and meninges such as cerebral shunts carry an increased risk of meningitis.
Bacterial and viral meningitis are contagious and can be transmitted through droplets of respiratory secretions during close contact such as kissing, sneezing, or coughing on someone, but cannot be spread by only breathing the air where a person with meningitis has been. Since the 1980’s, many countries have included immunization against Haemophilus influenzae type B in their routine childhood vaccination schemes. This has practically eliminated this pathogen as a cause of meningitis in young children in those countries.
Key Points
• Meningitis can be caused by viruses, bacteria, fungi, and protozoa.
• The most common symptoms of meningitis are headache and neck stiffness associated with fever, confusion or altered consciousness, vomiting, and an inability to tolerate light (photophobia) or loud noises (phonophobia).
• A lumbar puncture diagnoses or excludes meningitis.
• The first treatment in acute meningitis consists of antimicrobial and sometimes antiviral therapy.
Key Terms
• meninges: The three membranes that envelop the brain and spinal cord.
• meningitis: Inflammation of the meninges, characterized by headache, neck stiffness and photophobia and also fever, chills, vomiting, and myalgia.
• lumbar puncture: A diagnostic and at times therapeutic procedure performed to collect a sample of cerebrospinal fluid for biochemical, microbiological, and cytological analysis, or rarely to relieve increased intracranial pressure. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20C%3A_Meningitis.txt |
Learning Objectives
• Compare and contrast the three major modes of entry for Botulinium toxin (infant botulism or adult intestinal toxemia, foodborne botulism, and wound botulism) and describe its mechanism of action
Overview of Botulism
Botulism is a rare, but sometimes fatal, paralytic illness caused by botulinum toxin. It can affect a wide range of mammals, birds and fish. This toxin is a protein produced under anaerobic conditions by the bacterium Clostridium botulinum. The toxin enters the human body in one of three ways: by colonization of the digestive tract by the bacterium in children (infant botulism) or adults (adult intestinal toxemia), by ingestion of toxin from foods (foodborne botulism), or by contamination of a wound by the bacterium (wound botulism). Person-to-person transmission of botulism does not occur. All forms lead to paralysis that typically starts with the muscles of the face and then spreads towards the limbs. In severe forms, it leads to paralysis of the breathing muscles and causes respiratory failure. In light of this life-threatening complication, all suspected cases of botulism are treated as medical emergencies, and public health officials are usually involved to prevent further cases from the same source. Botulism can be prevented by killing the spores by pressure cooking or autoclaving at 121 °C (250 °F) for 30 minutes or providing conditions that prevent the spores from growing. Additional precautions for infants include not feeding them honey.
C. botulinum is an anaerobic, Gram positive, spore-forming rod. Botulinium toxin is one of the most powerful known toxins: about one microgram is lethal to humans. It acts by blocking nerve function (neuromuscular blockade) through inhibition of the release of the excitatory neurotransmitter acetyl choline from the presynaptic membrane of neuromuscular junctions in the somatic nervous system. This causes paralysis. Advanced botulism can cause respiratory failure by paralyzing the muscles of the chest, which can progress to respiratory arrest. In all cases, illness is caused by the botulinium toxin produced by the bacterium C. botulinum in anaerobic conditions, and not by the bacterium itself. The pattern of damage occurs because the toxin affects nerves that fire (depolarize) at a higher frequency first.
MODES OF ENTRY
Three main modes of entry for the toxin are known. The most common form in Western countries is infant botulism. This occurs in small children who are colonized with the bacterium during the early stages of their lives. The bacterium then releases the toxin into the intestine, which is absorbed into the bloodstream. The consumption of honey during the first year of life has been identified as a risk factor for infant botulism and it is a factor in a fifth of all cases. The adult form of infant botulism is termed adult intestinal toxemia, and is exceedingly rare. Foodborne botulism results from contaminated foodstuffs in which C. botulinum spores have been allowed to germinate in anaerobic conditions. This typically occurs in home-canned food substances and fermented uncooked dishes. Given that multiple people often consume food from the same source, it is common for more than a single person to be affected simultaneously. Symptoms usually appear 12–36 hours after eating, but can also appear within 6 hours to 10 days. Wound botulism results from the contamination of a wound with the bacteria, which then secrete the toxin into the bloodstream. This has become more common in intravenous drug users since the 1990s, especially people using black tar heroin and those injecting heroin into the skin rather than the veins
TREATMENT
The only drug currently available to treat infant botulism is Botulism Immune Globulin Intravenous-Human (BIG-IV or BabyBIG). BabyBIG was developed by the Infant Botulism Treatment and Prevention Program at the California Department of Public Health. There are two primary Botulinum Antitoxins available for treatment of wound and foodborne botulism. Trivalent (A,B,E) Botulinum Antitoxin is derived from equine sources utilizing whole antibodies (Fab & Fc portions). This antitoxin is available from the local health department via the CDC. The second antitoxin is heptavalent (A,B,C,D,E,F,G) Botulinum Antitoxin which is derived from “despeciated” equine IgG antibodies which have had the Fc portion cleaved off leaving the F(ab’)2 portions. This is a less immunogenic antitoxin that is effective against all known strains of botulism where not contraindicated. This is available from the US Army.
Key Points
• The toxin (s) enters the human body by colonization of the digestive tract by the bacterium, by ingestion of toxin from foods or by contamination of a wound by the bacterium.
• All forms lead to paralysis that typically starts with the muscles of the face and then spreads towards the limbs.
• Botulism can be prevented by killing the spores by pressure cooking or autoclaving at 121 °C (250 °F) for 30 minutes or providing conditions that prevent the spores from growing.
Key Terms
• infant botulism: poisoning caused by the toxin from Clostridium botulinum where the gastro-intestinal tract is colonized by spores prior to the protective intestinal bacterial flora having developed
• spore: A thick resistant particle produced by a bacterium or protist to survive in harsh or unfavorable conditions.
• botulism: Poisoning caused by the toxin from Clostridium botulinum, a type of anaerobic bacteria that grows in improperly-prepared food.
• wound botulism: poisoning caused by the toxin from Clostridium botulinum when spores enter a wound under the skin, and, in the absence of oxygen are activated and release toxin
• toxin: A toxic or poisonous substance produced by the biological processes of biological organisms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20D%3A_Botulism.txt |
Learning Objectives
• Describe the causative agents of leprosy: Mycobacterium leprae and Mycobacterium lepromatosis
Leprosy, also known as Hansen’s disease (HD), is a chronic disease caused by the bacteria Mycobacterium leprae and Mycobacterium lepromatosis. Named after physician Gerhard Armauer Hansen, leprosy is primarily a granulomatous disease of the peripheral nerves and mucosa of the upper respiratory tract. Skin lesions are the primary external sign. Left untreated, leprosy can be progressive, causing permanent damage to the skin, nerves, limbs, and eyes.
Diagnosis
Diagnosis in the U.S. is often delayed because healthcare providers are unaware of leprosy and its symptoms. Early diagnosis and treatment prevents nerve involvement, the hallmark of leprosy, and the disability it causes. There are many kinds of leprosy, but there are common symptoms, including:
• Runny nose
• Dry scalp
• Eye problems
• Skin lesions
• Muscle weakness
• Reddish skin
• Smooth, shiny, diffuse thickening of skin on the face, ears, and hands
• Loss of sensation in fingers and toes
• Thickening of peripheral nerves
• Flat nose due to destruction of nasal cartilage
There is also phonation and resonation of sound during speech. Often there is atrophy of the testes and impotency.
Causative Agents
Mycobacterium leprae and Mycobacterium lepromatosis are the causative agents of leprosy. M. lepromatosis is a comparatively recently identified mycobacterium that was isolated from a fatal case of diffuse lepromatous leprosy in 2008. An intracellular, acid-fast bacterium, M. leprae is aerobic and rod-shaped, and is surrounded by the waxy cell membrane coating characteristic of Mycobacterium species. Due to extensive loss of genes necessary for independent growth, M. leprae and M. lepromatosis are obligate pathogens, and are unculturable in the laboratory, a factor that leads to difficulty in definitively identifying the organism under a strict interpretation of Koch’s postulates. The use of non-culture-based techniques such as molecular genetics has allowed for alternative establishment of causation.
Routes of Infection
M. leprae is usually spread from person to person in respiratory droplets. Studies have shown that leprosy can be transmitted to humans through contact with armadillos, too. Leprosy is not known to be either sexually transmitted or highly infectious after treatment. Approximately 95% of people are naturally immune, and sufferers are no longer infectious after as little as two weeks of treatment. In 1988, Jacinto Convit was nominated for the Nobel Prize in Medicine for developing a vaccine to fight leprosy using a combination of tuberculosis (TB) vaccines with Mycobacterium Leprae. A number of synthetic pharmaceuticals that are effective against leprosy have now been identified, allowing doctors a flexible choice of treatments.
Key Points
• Left untreated, leprosy can be progressive, causing permanent damage to the skin, nerves, limbs, and eyes.
• M. leprae and M. lepromatosis are obligate pathogens, and are unculturable in the laboratory, a factor that leads to difficulty in definitively identifying the organism under a strict interpretation of Koch’s postulates.
• There is now a vaccination and extensive pharmaceutical options for treatment and prevention of leprosy.
Key Terms
• leprosy: Leprosy, also known as Hansen’s disease (HD), is a chronic disease caused by the bacteria Mycobacterium leprae and Mycobacterium lepromatosis.
• mycobacterium: Any of many rod-shaped, aerobic bacteria, of the genus Mycobacterium, that cause diseases such as tuberculosis and leprosy | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20E%3A_Leprosy.txt |
Tetanus is a medical condition characterized by a prolonged contraction of skeletal muscle fibers.
Learning Objectives
• Describe the mode of transmission and mechanism of action for Clostridium tetani
Key Points
• Infection generally occurs through wound contamination and often involves a cut or deep puncture wound.
• There are currently no blood tests that can be used to diagnose tetanus.
• Tetanus can be prevented by vaccination with tetanus toxoid.
Key Terms
• tetanus: A serious and often fatal disease caused by the infection of an open wound with the anaerobic bacterium Clostridium tetani, found in soil and the intestines and feces of animals.
• opisthotonos: A tetanic spasm in which the body is bent backwards and stiffened.
• neurotoxin: A toxin that specifically acts upon neurons, their synapses, or the nervous system in its entirety.
• tetanospasmin: The A-B toxin produced by C. tetani which is responsible for the symptoms of tetanus.
Overview
Tetanus is a medical condition characterized by a prolonged contraction of skeletal muscle fibers. The primary symptoms are caused by tetanospasmin, a neurotoxin produced by the Gram-positive, rod-shaped, obligate anaerobic bacterium Clostridium tetani.
Infection and Symptomatic Effects
Infection generally occurs through wound contamination and often involves a cut or deep puncture wound. C. tetani is not invasive, and the infection is normally confined to a wound. Here the bacteria multiply and produce tetanospasmin, which is able to travel throughout the body. Tetanospasmin is an A-B toxin. The B subunit binds to the receptors on motor neurons, while the A subunit induces endocytosis to enter the neuron. Early symptoms of the disease include restlessness, irritability and difficulty swallowing. As the infection progresses, muscle spasms develop in the jaw (thus the name “lockjaw”) and elsewhere in the body. Infection can be prevented by proper immunization and by post-exposure prophylaxis. Tetanus often begins with mild spasms in the jaw muscles (lockjaw). The spasms can also affect the chest, neck, back, and abdominal muscles. Back muscle spasms often cause arching, called opisthotonos. Prolonged muscular action causes sudden, powerful, and painful contractions of muscle groups. This is called tetany.
Tetanus affects skeletal muscle, a type of striated muscle used in voluntary movement. The other type of striated muscle, cardiac or heart muscle, is not affected by the toxin because of its intrinsic electrical properties. The incubation period of tetanus can be long, and may be as long several months, but is usually about eight days. In general, the further the injury site is from the central nervous system, the longer the incubation period. The shorter the incubation period, the more severe the symptoms.
Sources of Infection
Tetanus is often associated with rust, especially rusty nails, but this concept is somewhat misleading. Objects that accumulate rust are often found outdoors, or in places that harbor anaerobic bacteria, but the rust itself does not cause tetanus nor does it contain C. tetani bacteria. The rough surface of rusty metal merely provides a prime habitat for a C. tetani endospore to reside, and the nail affords a means to puncture skin and deliver endospore into the wound. An endospore is a non-metabolizing survival structure that begins to metabolize and cause infection once in an adequate environment. Because C. tetani is an anaerobic bacterium, it and its endospores survive well in an environment that lacks oxygen. Hence, stepping on a nail, rusty or not, may result in a tetanus infection, as the low-oxygen (anaerobic) environment is provided by the same object that causes a puncture wound, delivering endospores to a suitable environment for growth.
Diagnosis, Treatment, and Prevention
There are currently no blood tests that can be used to diagnose tetanus. The diagnosis is based on the presentation of tetanus symptoms. Diagnosis does not depend upon isolation of the bacteria, which is recovered from the wound in only 30% of cases and can be isolated from patients without tetanus. The “spatula test” is a clinical test for tetanus that involves touching the posterior pharyngeal wall with a sterile, soft-tipped instrument, and observing the effect. A positive test result is the involuntary contraction of the jaw (biting down on the “spatula”); a negative test result would normally be a gag reflex attempting to expel the foreign object.
Unlike many infectious diseases, recovery from naturally acquired tetanus does not usually result in immunity to tetanus. This is due to the extreme potency of the tetanospasmin toxin; even a lethal dose of tetanospasmin is insufficient to provoke an immune response.Tetanus can be prevented by vaccination with tetanus toxoid. The CDC recommends that adults receive a booster vaccine every ten years, and standard care practice in many places is to give the booster to any patient with a puncture wound who is uncertain of when he or she was last vaccinated, or if he or she has had fewer than three lifetime doses of the vaccine. The booster may not prevent a potentially fatal case of tetanus from the current wound as it can take up to two weeks for tetanus antibodies to form.
A person infected with C. tetani can be treated with antibiotics, which will kill the multiplying bacteria but will have no effect on the endospores or the toxin. To combat the effects of the toxin, tetanus immune globulin (TIG) antitoxin can be given to the patient. These antibodies are able to neutralize the tetanospasmin if they are not already bound to motor neurons, and can confer passive immunity. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20F%3A_Tetanus.txt |
Botulinum toxin is a protein and neurotoxin, which blocks neuromuscular transmission through decreased acetylcholine release.
Learning Objectives
• Describe the mechanism of action for botulinum toxin
Key Points
• Botulinum toxin is produced by Clostridium botulinum, C. butyricum, C. baratii and C. argentinense.
• The light chain of botulinum toxin is an enzyme (a protease ) that attacks one of the fusion proteins (SNAP-25, syntaxin or synaptobrevin) at a neuromuscular junction, preventing vesicles from anchoring to the membrane and releasing acetylcholine.
• The heavy chain of the toxin is particularly important for targeting the toxin to specific types of axon terminals.
Key Terms
• neurotoxin: A toxin that specifically acts upon neurons, their synapses, or the nervous system in its entirety.
• acetylcholine: A neurotransmitter in humans and other animals. It is an ester of acetic acid and choline with chemical formula CH3COOCH2CH2N<sup>+</sup>(CH3)3.
• axon: A nerve fibre, which is a long slender projection of a nerve cell, and which conducts nerve impulses away from the body of the cell to a synapse.
Botulinum toxin is a protein and neurotoxin produced by Clostridium botulinum, C. butyricum, C. baratii and C. argentinense. Botulinum toxin can cause botulism, a serious and life-threatening illness in humans and animals. In 1949, Arnold Burgen’s group discovered, through an elegant experiment, that botulinum toxin blocks neuromuscular transmission through decreased acetylcholine release. In 1973, Alan Scott used botulinum toxin type A (BTX-A) in monkey experiments. In 1980, he officially used BTX-A for the first time in humans to treat “crossed eyes” (strabismus), a condition in which the eyes are not properly aligned with each other, as well as “uncontrollable blinking” (blepharospasm). In 1993, Pasricha and colleagues showed that botulinum toxin could be used for the treatment of achalasia, a spasm of the lower esophageal sphincter. In 1994, Bushara showed botulinum toxin injections inhibit sweating; this was the first demonstration of non-muscular use of BTX-A in humans. The cosmetic effect of BTX-A on wrinkles was first reported by J. D. and J. A. Carruthers in a 1992 study on BTX-A for the treatment of glabellar frown lines. The acceptance of BTX-A use for the treatment of muscle pain disorders is growing, with approvals pending in many European countries. The efficacy of BTX-A in treating a variety of other medical conditions (including prostatic dysfunction, asthma, and others) is an area of continued study.
Foodborne botulism can be transmitted through food that has not been heated correctly prior to being canned, or food from a can that has not been cooked correctly. Most infant botulism cases cannot be prevented because the bacteria that cause this disease are in soil and dust. The bacteria can also be found inside homes on floors, carpet, and countertops, even after cleaning. Honey can contain the bacteria that cause infant botulism, so children less than 12 months old should not be fed honey.
Botulinum toxin is a two-chain polypeptide with a 100-kDa heavy chain joined by a disulfide bond to a 50-kDa light chain. This light chain is an enzyme (a protease) that attacks one of the fusion proteins (SNAP-25, syntaxin or synaptobrevin) at a neuromuscular junction, preventing vesicles from anchoring to the membrane to release acetylcholine. By inhibiting acetylcholine release, the toxin interferes with nerve impulses and causes flaccid (sagging) paralysis of muscles in botulism, as opposed to the spastic paralysis seen in tetanus. The heavy chain of the toxin is particularly important for targeting the toxin to specific types of axon terminals. The toxin must get inside the axon terminals to cause paralysis. Following the attachment of the toxin heavy chain to proteins on the surface of axon terminals, the toxin can be taken into neurons by endocytosis. The light chain is able to cleave endocytotic vesicles and reach the cytoplasm. The light chain of the toxin has protease activity. The type A toxin proteolytically degrades the SNAP-25 protein, a type of SNARE protein. The SNAP-25 protein is required for vesicle fusion that releases neurotransmitters from the axon endings (in particular acetylcholine). Botulinum toxin specifically cleaves these SNAREs, and so prevents neurosecretory vesicles from docking/fusing with the nerve synapse plasma membrane and releasing their neurotransmitters.
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• Botulinum toxin 3BTA. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Bo...toxin_3BTA.png. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.20%3A_Microbial_Diseases_of_the_Nervous_System/15.20G%3A_Paralysis-Causing_Bacterial_Neurotoxins.txt |
Rabies is a viral disease that causes acute encephalitis in warm-blooded animals.
Learning Objectives
• Examine the causes and symptoms associated with infection by the rabies virus
Key Points
• The rabies virus infects the central nervous system, travelling from the peripheral nerves to the brain.
• Symptoms include hydrophobia, paranoia, terror, mania, hallucinations, and delirium.
• Once symptoms have presented, survival is rare, but treatment administered before the onset of symptoms is highly successful.
Key Terms
• hydrophobia: An aversion to water, as a symptom of rabies.
• zoonotic: of or relating to zoonosis, the transmission of an infectious disease between species.
Rabies is a viral disease that causes acute encephalitis (inflammation of the brain) in warm-blooded animals. Rabies literally means “madness” in Latin. The disease is zoonotic and can be transmitted from one species to another, commonly by a bite from an infected animal. In humans, rabies is almost invariably fatal if postexposure prophylaxis is not administered prior to the onset of severe symptoms.
The rabies virus infects the central nervous system, travelling from the peripheral nerves to the brain. In humans, the incubation period between infection and the first sign of symptoms is typically two to 12 weeks, although periods as short as four days and longer than six years have been documented. Incubation period depends on the quantity of virus introduced and the distance it must travel to reach the central nervous system. Once there, symptoms begin to show and the infection is virtually untreatable. Early-stage symptoms include malaise, headache and fever, violent movements, uncontrolled excitement, depression, confusion, agitation, anxiety, and hydrophobia. Late stage symptoms extend to paranoia, terror, mania, and hallucinations progressing into delirium. Once symptoms have presented, survival is rare. Death almost invariably occurs within two to 10 days. Treatment with human rabies immunoglobulin (HRIG) and rabies vaccine is highly successful if administered before the onset of symptoms.
Rabies causes about 55,000 human deaths annually worldwide, with 95% of human deaths occurring in Asia and Africa. Roughly 97% of human rabies cases result from dog bites. In the U.S., animal control and vaccination programs have effectively eliminated domestic dogs as reservoirs of rabies. In several countries, including Australia and Japan, rabies carried by terrestrial animals has been eliminated entirely. While rabies was once eradicated in the United Kingdom, infected bats have recently been found in Scotland. In the U.S., the widespread vaccination of domestic dogs and cats and the development of effective human vaccines and immunoglobulin treatments has dropped the number of recorded human deaths from 100 or more annually in the early 20th century, to one to two per year (mostly caused by bat bites). Modern cell-based vaccines are similar to flu shots in terms of pain and side effects. The old nerve-tissue-based vaccinations that require multiple painful injections into the abdomen with a large needle are cheap, but are being phased out and replaced by affordable World Health Organization intradermal vaccination regimens.
Rabies may be diagnosed by PCR or viral culture of brain samples after death, or from skin samples taken before. Diagnosis can be made from saliva, urine, and cerebrospinal fluid samples with less accuracy. Cheaper rabies diagnosis will become possible for low-income settings using basic light microscopy techniques. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21A%3A_Rabies.txt |
Poliomyelitis is an infection by the polio virus that affects the motor neurons of the central nervous system.
Learning Objectives
• Describe poliomyelitis and its effect on motor neurons
Key Points
• Spinal polio is the most common type of polio and results in asymmetric paralysis, usually involving the legs.
• Bulbar polio is infection of the cranial nerves and causes weakness and paralysis in muscles innervated by the cranial nerves, while bulbospinal polio occurs when both the cranial nerves and spinal nerves are affected.
• Although approximately 90% of polio infections cause no symptoms at all, affected individuals can exhibit a range of symptoms if the virus enters the blood stream.
Key Terms
• motor neuron: A neuron located in the central nervous system that projects its axon outside the CNS and directly or indirectly control muscles.
• spinal polio: Spinal polio is characterized by asymmetric paralysis that most often involves the legs.
• poliomyelitis: acute infection by the poliovirus, especially of the motor neurons in the spinal cord and brainstem, leading to muscle weakness, paralysis and sometimes deformity
• paralysis: The complete loss of voluntary control of part of person’s body, such as one or more limbs.
OVERVIEW
Poliomyelitis, often called polio or infantile paralysis, is an acute, viral, infectious disease spread from person to person, primarily via the fecal-oral route.
Although approximately 90% of polio infections cause no symptoms at all, affected individuals can exhibit a range of symptoms if the virus enters the blood stream. In about 1% of cases, the virus enters the central nervous system, preferentially infecting and destroying motor neurons, leading to muscle weakness and acute flaccid paralysis.
Different types of paralysis may occur, depending on the nerves involved. Spinal polio is the most common form, characterized by asymmetric paralysis that most often involves the legs. Bulbar polio leads to weakness of muscles innervated by cranial nerves. Bulbospinal polio is a combination of bulbar and spinal paralysis.
BACKGROUND
Poliomyelitis was first recognized as a distinct condition by Jakob Heine in 1840. Its causative agent, poliovirus, was identified in 1908 by Karl Landsteiner. Although major polio epidemics were unknown before the late 19th century, polio was one of the most dreaded childhood diseases of the 20th century. Polio epidemics have crippled thousands of people, mostly young children; the disease has caused paralysis and death for much of human history.
Polio had existed for thousands of years quietly as an endemic pathogen until the 1880s, when major epidemics began to occur in Europe; soon after, widespread epidemics appeared in the United States. By 1910, much of the world experienced a dramatic increase in polio cases and epidemics became regular events, primarily in cities during the summer months. These epidemics—which left thousands of children and adults paralyzed—provided the impetus for a “Great Race” towards the development of a vaccine.
DEVELOPMENT OF A VACCINE
Developed in the 1950s, polio vaccines are credited with reducing the global number of polio cases per year from many hundreds of thousands to today under a thousand. Enhanced vaccination efforts led by the World Health Organization, UNICEF, and Rotary International could result in global eradication of the disease. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21B%3A_Poliomyelitis.txt |
Hantaviruses are negative-sense RNA viruses that sometimes lead to hemorrhagic fever with renal syndrome in humans.
Learning Objectives
• Paraphrase the causes of hantavirus and the phases of symptoms: febrile, hypotensive, oliguric, diuretic and convalescent
Key Points
• The name hantavirus comes from the Hantaan River area in South Korea, where the first known strain – Hantaan virus (HTNV) – was isolated in 1978.
• Human infections of hantaviruses have almost entirely been linked to human contact with rodent excrement, thus, rodent control is the primary strategy for preventing hantavirus infection.
• There is no known antiviral treatment, but natural recovery from the virus is possible.
Key Terms
• hypoxemia: an abnormal deficiency in the concentration of oxygen in the blood, be it the partial pressure of oxygen (mm Hg), the content of oxygen (ml oxygen per dl of blood) or the percent saturation of the blood’s hemoglobin, singly or in combination.
• tachycardia: a rapid resting heart rate, especially one above 100 beats per minute.
• proteinuria: excessive protein in the urine.
Hantaviruses are negative sense RNA viruses and are a relatively newly discovered genus in the Bunyaviridae family. The name hantavirus comes from the Hantaan River area in South Korea, where the first known strain – Hantaan virus (HTNV) – was isolated in 1978. Although some hantaviruses lead to potentially fatal diseases, such as hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS), not all are associated with human disease.
Human infections of hantaviruses have almost entirely been linked to human contact with rodent excrement, thus, rodent control is the primary strategy for preventing hantavirus infection. Human-to-human transmission (via urine, saliva, etc. ) may also occur, and has been recently reported with the Andes virus in South America.
HTNV is one of several hantaviruses that cause hemorrhagic fever with renal syndrome (HFRS), formerly known as Korean hemorrhagic fever. HFRS has an incubation time of two to four weeks in humans before symptoms of infection occur. The symptoms of HFRS can be split into five phases: febrile, hypotensive, oliguric, diuretic, and convalescent. The febrile phase begins two to three weeks after exposure, and normally lasts from three to seven days. Symptoms include fever, chills, diarrhea, malaise, headaches, nausea, abdominal and back pain, and respiratory and gastro-intestinal problems. These symptoms can resemble that of the flu. The hypotensive phase occurs when the blood platelet levels drop, and can lead to tachycardia and hypoxemia. This phase can last for 2 days. The oliguric phase begins with renal failure and proteinuria, and lasts from three to seven days. The diuretic phase is characterized by excessive urination (diuresis) of up to six liters per day, and can last for a couple of days up to a week. Although there is no known antiviral treatment for hantavirus, natural recovery is possible. The phase where symptoms begin to improve is the convalescent phase.
Hantavirus pulmonary syndrome (HPS) is another potentially fatal disease caused by hantavirus infection. Although rare, HPS is fatal in up to 60% of cases. HPS has been identified throughout the United States, and was first recognized in 1993 in the southwest where it was originally referred to as the “Four Corners disease. ” The symptoms are very similar to those of HFRS. Additionally, patients will develop difficulty breathing, coughing and shortness of breath, and may lead to cardiovascular shock. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21C%3A_Hantavirus.txt |
Arboviral encephalitis (acute swelling in the brain) is caused by a group of arthropod-transmitted viruses.
Learning Objectives
• Examine the mode of transmission and causes of arboviral encephalitis
Key Points
• Arthropod vectors transmit the virus upon biting, allowing the virus to enter the circulatory system and replicate.
• Arboviral encephalitis are found in many places throughout the world, and include California encephalitis, Japanese encephalitis, St. Louis encephalitis, Tick-borne encephalitis, and West Nile fever.
• TBE Infection can be reliably prevented by vaccination, but is incurable once manifested.
Key Terms
• sequelae: A pathological condition resulting from a disease, injury, or other trauma.
• encephalitis: an inflammation of the brain
• viremia: A medical condition where viruses enter the bloodstream and hence have access to the rest of the body.
• zoonotic: of or relating to zoonosis, the transmission of an infectious disease between species.
Arboviral encephalitis are a group of arthropod-transmitted viruses that cause encephalitis (acute swelling in the brain). The word “arbovirus” directly refers to an ARthropod-BOrne virus. Arthropod vectors transmit the virus upon biting, allowing the virus to enter the circulatory system and replicate and shed additional infection into the bloodstream ( viremia ).
The majority of the arboviruses are spherical in shape although a few are rod-shaped. They are 17-150 nm in diameter and most have an RNA genome (the single exception is African swine fever virus, which has a DNA genome). Many arboviruses (such as African Swine Fever virus) do not infect humans or cause only mild and transient infections characterized by fever, headache, and rash. Those of the arboviral encephalitis group, however, can cause epidemic disease and severe infections that can be fatal. Arboviral encephalitis are found in many places throughout the world, and include California encephalitis, Japanese encephalitis, St. Louis encephalitis, Tick-borne encephalitis, and West Nile fever.
Tick-borne encephalitis (TBE) is an infectious disease of the central nervous system. It can infect a range of hosts including ruminants, birds, rodents, carnivores, horses, and humans. The disease can be zoonotic, with ruminants and dogs providing the principal source of infection for humans. TBE is transmitted through the bite of several species of infected ticks, including Ixodes scapularis, Ixodes ricinusand Ixodes persulcatus, and manifests most often as meningitis, encephalitis, or meningoencephalitis.
TBE Infection can be reliably prevented by vaccination, but is incurable once manifested. Long-lasting or permanent neuropsychiatric sequelae are observed in 10-20% of infected patients; morality occurs in only 1-2% of the infected, with deaths occurring 5 to 7 days after the onset of neurologic symptoms.
TBE and other arboviral encephalitis can be diagnosed through a combination of blood tests, particularly immunologic, serologic, and/or virologic techniques such as ELISA, complement fixation, polymerase chain reaction, Neutralization test, and Hemoagglutination Inhibition test.
Because the arboviral encephalitides are viral diseases, antibiotics are not effective for treatment and no effective antiviral drugs have been discovered yet. Treatment is therefore only supportive, attempting to deal with problems such as swelling of the brain, loss of the automatic breathing, activity of the brain, and other treatable complications like bacterial pneumonia.
Therefore, the immune system plays an important role in defense against arbovirus infections. Arboviruses usually stimulate the production of interferons and antibodies, which help to diminish the extent of viremia. Cell-mediated immunity is also important. Increased immunity is observed with age progression.
Vector control measures, such as habitat control (including the elimination of stagnant water and the spraying of insecticides), are essential to reducing the transmission of disease by arboviruses. People can also reduce the risk of getting bitten by arthropods by employing personal protective measures such as sleeping under mosquito nets, wearing protective clothing, applying insect repellents, tick-checks, and avoiding areas known to harbor high arthropod populations.
15.21E: Rickettsial Diseases
Rickettsia is a genus of bacteria that can be transmitted by arthropod vectors to humans, causing diseases.
Learning Objectives
• List the characteristics of Rickettsia species
Key Points
• Rickettsia are obligate intracellular parasites, and must replicate within the cytoplasm of eukaryotic host cells.
• Rickettsia species are carried by many ticks, fleas, and lice, and cause diseases in humans such as typhus, rickettsialpox, Boutonneuse fever, African tick bite fever, Rocky Mountain spotted fever, Flinders Island spotted fever, and Queensland tick typhus (Australian Tick Typhus).
• Rickettsia are one of closest living relatives to bacteria that were the origin of the mitochondria organelle that exists inside most eukaryotic cells. Indeed, certain segments of Rickettsia genomes resemble that of mitochondria, and ATP production is the same as that in mitochondria.
Key Terms
• parthenogenesis: a form of asexual reproduction in which growth and development of embryos occurs without fertilization.
• pleomorphic: the ability to alter shape or size in response to environmental conditions.
Rickettsia is a genus of bacteria that can be transmitted by arthropod vectors to humans, causing disease. Rickettsia species are non-motile, Gram-negative, non-sporeforming, highly pleomorphic bacteria that can present as cocci (0.1 μm in diameter), rods (1–4 μm long), or thread-like (10 μm long). They are obligate intracellular parasites, and must replicate within the cytoplasm of eukaryotic host cells. Rickettsia are one of closest living relatives to bacteria that were the origin of the mitochondria organelle that exists inside most eukaryotic cells. Unlike viruses, Rickettsia possess true cell walls and are similar to other gram-negative bacteria. Despite a similar name, Rickettsia bacteria do not cause rickets, which is a result of vitamin D deficiency.
Rickettsia species are carried by many ticks, fleas, and lice, and cause diseases in humans such as typhus, rickettsialpox, Boutonneuse fever, African tick bite fever, Rocky Mountain spotted fever, Flinders Island spotted fever, and Queensland tick typhus (Australian Tick Typhus). They have also been associated with a range of plant diseases.
Rickettsia can be classified into three groups based on serology and DNA sequencing: spotted fever, typhus, and scrub typhus. All three of these groups contain human pathogens. Recent studies reclassify the scrub typhus group as a new genus – Orienta, and suggest that the spotted fever group should be divided into two clades. Rickettsia are widespread, and can be associated with arthropods, leeches, and protists. Rickettsia found in Arthropods are generally associated with reproductive manipulation (such as parthenogenesis) to persist in host lineage.
Unlike free-living bacteria, Rickettsia species contain no genes for anaerobic glycolysis or those involved in the biosynthesis and regulation of amino acids and nucleosides. In this regard, certain segments of Rickettsia genomes resemble that of mitochondria, and ATP production is the same as that in mitochondria. (With the exception of R. prowazekii, whose genome contains a complete set of genes encoding for the tricarboxylic acid cycle and the respiratory chain complex). The genomes of both Rickettsia and mitochondria are frequently said to be “small, highly derived products of several types of reductive evolution. ” | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21D%3A_Arboviral_Encephalitis.txt |
Lyme disease is caused by bacteria from the Borrelia genus.
Learning Objectives
• Discuss the mode of transmission and symptoms for lyme disease
Key Points
• Borrelia is transmitted to humans through the bite of infected ticks belonging to a few species of the genus Ixodes (“hard ticks”).
• Lyme disease can affect multiple body systems and produce a range of symptoms.
• Lyme disease begins with a characterized bullseye rash called erythema chronicum migrans.
Key Terms
• nymphal: In some invertebrates, of or pertaining to the immature form.
• asymptomatic: not exhibiting any symptoms of disease.
• paraplegia: A condition where the lower half of a patient’s body is paralyzed and cannot move.
Lyme disease (aka Lyme borreliosis) is caused by bacteria from the Borrelia genus, and is the most common tick-borne disease in the Northern Hemisphere. Borrelia burgdorferi sensu stricto is the main cause of Lyme disease in North America, whereas Borrelia afzelii and Borrelia garinii cause most European cases. Borrelia is transmitted to humans through the bite of infected ticks belonging to a few species of the genus Ixodes (“hard ticks” ). The disease is named after the towns of Lyme and Old Lyme, Connecticut, where a number of cases were identified in 1975. Although it was realized that Lyme disease was a tick-borne disease in 1978, the cause of the disease remained a mystery until 1981, when B. burgdorferi was identified.
Lyme disease can affect multiple body systems and produce a range of symptoms, though not all patients with Lyme disease will have all symptoms, and many of the symptoms are not specific to Lyme disease. The incubation period from infection to the onset of symptoms is usually one to two weeks, but can be much shorter (days), or much longer (months to years). Most infections are caused by ticks in the nymphal stage, as they are very small and may feed undetected for long periods of time, with symptoms occurring most often from May through September because of this life cycle. An infected tick must be attached for at least a day for transmission to occur, and only about 1% of recognized tick bites result in Lyme disease.
Lyme disease begins with a localized infection, affecting the area at the site of the tick bite with a circular, outwardly expanding rash called erythema chronicum migrans (EM), which gives the appearance of a bullseye. Patients may also experience flu-like symptoms, such as headache, muscle soreness, fever, malaise, fatigue, and depression. In most cases, the infection and its symptoms are eliminated by antibiotics, especially if the illness is treated early. Delayed or inadequate treatment can lead to more serious symptoms, which can be disabling and difficult to treat. Asymptomatic infections may occur, though this is the case in less than 7% of infected individuals in the United States. Asymptomatic infection may be more common in Europe.
Left untreated, Borrelia bacteria begins to spread through the bloodstream within days to weeks after the onset of local infection, progressing symptoms to the joints, heart, and central nervous system. These symptoms include migrating pain in muscles, joints, and tendons; neck stiffness; sensitivity to light; and heart palpitations and dizziness caused by changes in heartbeat. Acute neurological problems, termed “neuroborreliosis”, appear in 10–15% of untreated patients. EM may even develop at sites across the body that bear no relation to the original tick bite. Radiculoneuritis causes shooting pains that may interfere with sleep, as well as abnormal skin sensations. Mild encephalitis may lead to memory loss, sleep disturbances, or mood changes.
After several months, untreated or inadequately treated patients may go on to develop severe and chronic symptoms, including permanent paraplegia in the most extreme cases. Patients may develop Lyme arthritis, usually affecting the knees; nerve pain radiating out of the spine (Bannwarth syndrome); and shooting pains, numbness, and tingling in the hands or feet. A neurologic syndrome called Lyme encephalopathy is associated with subtle cognitive problems, such as difficulties with concentration and short-term memory. These patients may experience profound fatigue. Chronic encephalomyelitis can involve cognitive impairment, weakness in the legs, awkward gait, facial palsy, bladder problems, vertigo, and back pain. In rare cases, untreated Lyme disease may cause frank psychosis, which has been mis-diagnosed as schizophrenia or bipolar disorder. Panic attacks and anxiety can occur; as well as delusional behavior and detachment from themselves and reality. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21F%3A_Lyme_Disease.txt |
West Nile virus is a mosquito-borne arbovirus found in temperate and tropical regions of the world.
Learning Objectives
• Discuss the causes, symptoms and diseases (West Nile encephalitis, meningitis, meningoencephalitis and poliomyelitis) caused by the West Nile virus (WNV)
Key Points
• WNV is considered to be an endemic pathogen in Africa, Asia, Australia, the Middle East, Europe and in the United States, with one of the worst epidemics occurring in 2012.
• Birds are the most commonly infected animal, and serve as the prime reservoir host.
• The specific neurological diseases which may occur are encephalitis, meningitis, meningoencephalitis, and poliomyelitis.
Key Terms
• zoonotic: of or relating to zoonosis, the transmission of an infectious disease between species.
West Nile virus (WNV) is a mosquito-borne zoonotic arbovirus belonging to the genus Flavivirus, and is found in temperate and tropical regions of the world.
WNV was first identified in the West Nile subregion in the East African nation of Uganda in 1937. Prior to the mid 1990s, WNV disease occurred only sporadically and was considered a minor risk for humans. This was until an outbreak in Algeria in 1994, with cases of WNV-caused encephalitis, and the first large outbreak in Romania in 1996, with a high number of cases with neuroinvasive disease. WNV has now spread globally, with the first case in the Western Hemisphere being identified in New York City in 1999. The virus has now spread across the continental United States, north into Canada, and southward into the Caribbean Islands and Latin America. The US experienced one of its worst epidemics to date in 2012. WNV also spread to Europe, beyond the Mediterranean Basin, with a new strain of the virus recently identified in Italy (2012). WNV is now considered to be an endemic pathogen in Africa, Asia, Australia, the Middle East, Europe and in the United States.
The main mode of WNV transmission is by mosquitoes, the prime vector. WNV has been found in various species of ticks. However, current research suggests they are not important vectors of the virus. WNV infects various mammal species, including humans. It has also been identified in reptilians (including alligators and crocodiles) and amphibians. Birds, especially passerines, are the most commonly infected animal, and serve as the prime reservoir host. Many species – including humans – do not develop viral levels sufficient to transmit the disease to uninfected mosquitoes, and are thus not considered major factors in WNV transmission.
Approximately 80% of West Nile virus infections in humans cause no symptoms. West Nile fever is the manifestation of symptoms, with an incubation period typically between 2 and 15 days. Symptoms may include fever, headaches, fatigue, muscle pain or aches, malaise, nausea, anorexia, vomiting, myalgias and rash. Less than 1% of the cases are severe and result in neurological disease when the central nervous system is affected. People of advanced age, the very young, or those with immunosuppression are most susceptible.
The specific neurological diseases which may occur are:
• West Nile encephalitis, which causes inflammation of the brain
• West Nile meningitis, which causes inflammation of the meninges (the protective membranes that cover the brain and spinal cord)
• West Nile meningoencephalitis, which causes inflammation of the brain and surrounding meninges
• West Nile poliomyelitis (spinal cord inflammation, which results in a syndrome similar to polio that may cause acute flaccid paralysis).
Currently, no vaccine against WNV infection is available. The best method to reduce the rates of WNV infection is by public mosquito control (particularly the elimination of standing water) and by personal protection (mosquito nets and repellent). | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.21%3A_Other_Diseases_of_the_Nervous_System/15.21G%3A_West_Nile_Virus.txt |
The plague is an infectious disease caused by the Gram-negative rod-shaped bacteria Yersinia pestis.
Learning Objectives
• Outline the route of pathogenesis for Yersinia pestis
Key Points
• Although bubonic plague is often used synonymously with plague, it refers specifically to an infection that enters through the skin and travels through the lymph nodes (buboes).
• Septicemic plague is a deadly blood infection; symptoms include hypotension, hepatosplenomegaly, delirium, seizures in children, shock, lethargy, and fever. Pneumonic plague manifests as a severe lung infection.
• Y. pestis is spread most commonly between rodents (both urban and wild) and fleas.
Key Terms
• pneumonic plague: a severe type of lung infection, one of three main forms of plague, all of which are caused by the bacterium Yersinia pestis
• bubonic plague: a contagious, often fatal, epidemic disease caused by the bacterium Yersinia pestis, transmitted by the bite of fleas from an infected person or rodent, especially a rat, and characterized by delirium, chills, fever, vomiting, diarrhea, and the formation of buboes
• hepatosplenomegaly: enlargement of both the liver and spleen.
• plague: an epidemic or pandemic caused by any pestilence, but specifically by the above disease
The plague is an infectious disease caused by the Gram-negative rod-shaped bacteria Yersinia pestis . Human Y. pestis infection is manifested in three main forms: pneumonic, septicemic, and the notorious bubonic plagues. All three forms are widely believed to have been responsible for a number of high-mortality epidemics throughout human history, including the Plague of Justinian in 542, and the Black Death that accounted for the death of at least one-third of the European population between 1347 and 1353. It has now been conclusively shown that these plagues originated in rodent populations in China. Thousands of cases of the plague are still reported every year; with proper treatment, the prognosis for victims is now much improved. The plague also has a detrimental effect on non-human mammals. In the United States, animals such as the black-tailed prairie dog and the endangered black-footed ferret are under threat from the disease.
Although bubonic plague is often used synonymously with plague, it refers specifically to an infection that enters through the skin and travels through the lymph nodes (buboes). The incubation period of bubonic plague is from 2-6 days, while the bacteria actively replicate. Symptoms include a lack of energy, fever, headache and chills, and swelling of lymph nodes resulting in buboes, the classic sign of bubonic plague. Septicemic plague is a deadly blood infection; symptoms include hypotension, hepatosplenomegaly, delirium, seizures in children, shock, lethargy, and fever. Pneumonic plague manifests as a severe lung infection, and is more virulent and rare than bubonic plague. Symptoms include fever, chills, coughing, chest pain, dyspnea, hemoptysis, lethargy, hypotension, and shock. Symptoms of the plague are not always present, or the patient may die before any symptoms appear.
Y. pestis is spread most commonly between rodents (both urban and wild) and fleas. Any infected animal can transmit the infection to humans through contact with skin tissue. Humans can also spread the bacteria to other humans through sneezing, coughing, or with direct contact with infected tissue. The reservoir commonly associated with Y. pestis is several species of rodents. In the steppes, the reservoir species is believed to be principally the marmot. In the United States, several species of rodents are thought to maintain Y. pestis. However, the expected disease dynamics have not been found in any rodent species. It is known that rodent populations will have a variable resistance, which could lead to a carrier status in some individuals. In some regions of the world, the reservoir of infection is not clearly identified, which complicates prevention and early warning programs.
The transmission of Y. pestis by fleas is well characterized. Initial acquisition of Y. pestis by the vector occurs during feeding on an infected animal. Several proteins then contribute to the maintenance of the bacteria in the flea digestive tract, among them the hemin storage (Hms) system and Yersinia murine toxin (Ymt). Although Yersinia murine toxin is highly toxic to rodents and was once thought to be produced to ensure reinfection of new hosts, it has been demonstrated that Ymt is important for the survival of Y. pestis in fleas. The Hms system plays an important role in the transmission of Y. pestis back to a mammalian host. While in the insect vector, proteins encoded by Hms genetic loci induce biofilm formation in the proventriculus, a valve connecting the midgut to the esophagus. Aggregation in the biofilm inhibits feeding, as a mass of clotted blood and bacteria forms (referred to as “Bacot’s block”). Transmission of Y. pestis occurs during the futile attempts of the flea to feed. Ingested blood is pumped into the esophagus, where it dislodges bacteria lodged in the proventriculus and is regurgitated back into the host circulatory system.
The pathogenesis of Y. pestis infection in mammalian hosts is due to several factors. The bacteria proliferates inside lymph nodes where it is able to avoid destruction by cells of the immune system such as macrophages. Y. pestis is able to suppress the immune system, avoiding normal immune system responses such as phagocytosis and antibody production. Flea bites allow for the bacteria to pass the skin barrier. Y. pestis expresses the yadBC gene, which is similar to adhesins in other Yersinia species, allowing for adherence and invasion of epithelial cells. Finally, Y. pestis expresses a plasminogen activator that is an important virulence factor for pneumonic plague, which may also degrade on blood clots in order to facilitate systematic invasion. Two important anti-phagocytic antigens, Fraction 1 (F1) and LcrV (V), are both important for virulence. Natural or induced immunity is achieved, therefore, by the production of specific opsonic antibodies against F1 and V antigens.
The traditional first line treatment for Y. pestis has been the antibiotics streptomycin, chloramphenicol, tetracycline, and fluoroquinolones. Antibiotic treatment alone is insufficient for some patients, who may also require circulatory, ventilator, or renal support.
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Cryptococcosis is a disease caused by fungi that can be fatal.
Learning Objectives
• Recognize the causes and symptoms associated with cryptococcosis
Key Points
• Cryptococcal meningitis is caused when the disease-causing fungus gets in the membranes around the brain.
• Cryptococcosis is an opportunistic infection, it often affects people who are immune -compromised, such as people who have AIDS.
• As people who get cryptoccosis often have other health problems, even treatment with anti- fungal agents may not cure the infection.
• Cryptococcosis can infect animals such as cats; it is not solely a human pathogen.
Key Terms
• meninges: The three membranes that envelop the brain and spinal cord.
• propagule: A reproductive particle released by an organism that may germinate into another.
Cryptococcosis, or cryptococcal disease, is a potentially fatal fungal disease. It is caused by one of two species: Cryptococcus neoformans and Cryptococcus gattii. These were all previously thought to be subspecies of C. neoformans, but have now been identified as distinct species. Cryptococcosis is believed to be acquired by inhalation of the infectious propagule from the environment. Although the exact nature of the infectious propagule is unknown, the leading hypothesis is the basidiospore created through sexual or asexual reproduction.
Causes
Cryptococcal meningitis (infection of the meninges, the tissue covering the brain) is believed to result from dissemination of the fungus from either an observed or unappreciated pulmonary infection. Often there is also silent dissemination throughout the brain when meningitis is present. Cryptococcus gattii causes infections in immunocompetent people (those having a functioning immune system), but C. neoformans v. grubii, and v. neoformans usually only cause clinically evident infections in persons who have some form of defect in their immune systems ( immunocompromised persons). People who have defects in their cell-mediated immunity; for example, people with AIDS; are especially susceptible to disseminated cryptococcosis. Cryptococcosis is often fatal, even if treated. The ten-week survival averages near 70% with optimal therapy.
Although the most common presentation of cryptococcosis is of C. neoformans infection in an immunocompromised person (such as persons living with AIDS), the C. gattii is being increasingly recognised as a pathogen in presumptively immunocompetent hosts, especially in Canada and Australia. This may be due to rare exposure and high pathogenicity, or to unrecognised isolated defects in immunity, specific for this organism.
Cryptococcosis is a defining opportunistic infection for AIDS. Other conditions which pose an increased risk include certain lymphomas (e.g. Hodgkin’s lymphoma), sarcoidosis, liver cirrhosis, and patients on long-term corticosteroid therapy. Distribution is worldwide in soil. The prevalence of cryptococcosis has been increasing over the past 20 years for many reasons, including the increase in incidence of AIDS and the expanded use of immunosuppressive drugs.
Treatment
Treatment options in non-AIDS patients who have reduced immune-system function is not well studied. Intravenous Amphotericin B combined with oral flucytosine may be effective. Every attempt should be made to reduce the amount of immunosuppressive medication until the infection is resolved. Persons living with AIDS often have a greater chance of disease and higher mortality (30-70% at ten-weeks), but recommended therapy is with antifungal agents such as Amphotericin B and flucytosine.
Cryptococcosis in Animals
Cryptococcosis is also seen in cats and occasionally dogs. It is the most common deep fungal disease in cats, usually leading to chronic infection of the nose and sinuses, and skin ulcers. Cats may develop a bump over the bridge of the nose from local tissue inflammation. It can be associated with feline leukemia virus infection in cats. Cryptococcosis is most common in dogs and cats, but cattle, sheep, goats, horses, wild animals and birds can also be infected. Soil, fowl manure, and pigeon droppings are among the sources of infection. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.22%3A_Fungal_Protozoan_Prion_and_Other_Diseases_of_the_Nervous_System/15.22A%3A_Cryptococcosis.txt |
Sleeping sickness is caused by a protozoa transmitted by the tsetse fly.
Learning Objectives
• Outline the life cycle of Trypanosoma brucei and its route of transmission that causes African trypanosomiasis
Key Points
• The disease is caused by protozoa of the species Trypanosoma brucei, which in a mammalian blood system become a trypomastigote and travels throughout the host mammalian and infects spinal fluid and lymph nodes.
• The protozoa Trypanosoma brucei infects the tsetse fly when it feeds on the blood of an infected mammal. Once infected a tsetse fly can transmit the disease to other mammals.
• Initially, sleeping sickness has many symptoms of other viral infections, but if left untreated it will affect the nervous system, causing lethargy.
Key Terms
• trypomastigote: A stage in unicellular life-cycle, typically trypanosomes, where the flagellum is posterior of the nucleus, and connected to the cell body by a long undulating membrane.
• epimastigotes: A stage in unicellular life-cycle, typically trypanosomes, where the flagellum is anterior of the nucleus, and attached the cell body by a short membrane.
Human African trypanosomiasis, sleeping sickness, African lethargy, or Congo trypanosomiasis is a parasitic disease of people and animals, caused by protozoa of the species Trypanosoma brucei and transmitted by the tsetse fly. The disease is endemic in some regions of sub-Saharan Africa, covering areas in about 37 countries containing more than 60 million people. An estimated 50-70 thousand people are currently infected, the number having declined somewhat in recent years. The number of reported cases was below ten thousand in 2009, the first time in 50 years. Many cases are believed to go unreported. About 48 thousand people died of it in 2008. Four major epidemics have occurred in recent history: one from 1896-1906, primarily in Uganda and the Congo Basin, two epidemics in 1920 and 1970 in several African countries, and a recent 2008 epidemic in Uganda.
Transmission
The tsetse fly (genus Glossina) is a large, brown, biting fly that serves as both a host and vector for the trypanosome parasites. While taking blood from a mammalian host, an infected tsetse fly injects metacyclic trypomastigotes into skin tissue. From the bite, parasites first enter the lymphatic system and then pass into the bloodstream. Inside the mammalian host, they transform into bloodstream trypomastigotes, and are carried to other sites throughout the body, reach other body fluids (e.g., lymph, spinal fluid), and continue to replicate by binary fission. The entire life cycle of African trypanosomes is represented by extracellular stages. A tsetse fly becomes infected with bloodstream trypomastigotes when taking a blood meal on an infected mammalian host. In the fly’s midgut, the parasites transform into procyclic trypomastigotes, multiply by binary fission, leave the midgut, and transform into epimastigotes. The epimastigotes reach the fly’s salivary glands and continue multiplication by binary fission.The entire life cycle of the fly takes about three weeks.
In addition to the bite of the tsetse fly, the disease can be transmitted by, mother-to-child infection; the trypanosome can sometimes cross the placenta and infect the fetus. Transmission can also occur in laboratories by accidental infections; for example, through the handling of blood of an infected person and organ transplantation, though this is uncommon. Blood transfusions and possibly sexual contact, are two other causes.
Symptoms
African trypanosomiasis symptoms occur in two stages. The first stage, known as the haemolymphatic phase, is characterized by fever, headaches, joint pains, and itching. Invasion of the circulatory and lymphatic systems by the parasites is associated with severe swelling of lymph nodes, often to tremendous sizes. If left untreated, the disease overcomes the host’s defenses and can cause more extensive damage, broadening symptoms to include anemia, endocrine, cardiac, and kidney dysfunctions. The second phase, the neurological phase, begins when the parasite invades the central nervous system by passing through the blood–brain barrier. The term “sleeping sickness” comes from the symptoms of the neurological phase. The symptoms include confusion, reduced coordination, and disruption of the sleep cycle, with bouts of fatigue punctuated with manic periods, leading to daytime slumber and night-time insomnia. Without treatment, the disease is invariably fatal, with progressive mental deterioration leading to coma and death. Damage caused in the neurological phase is irreversible. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.22%3A_Fungal_Protozoan_Prion_and_Other_Diseases_of_the_Nervous_System/15.22B%3A_African_Trypanosomiasis.txt |
Amoebic meningoencephalitis is an often-fatal central nervous system infection caused by Naegleria fowleri.
Learning Objectives
• Summarize the route of transmission and effects of infection by Naegleria fowleri
Key Points
• Amoebic meningoencephalitis is not actually caused by an ameoba but rather Naegleria fowleri a protist found in warm fresh water.
• Once Naegleria fowleri enters deep into the nasal passage, digesting through the olfactory bulbs it then migrates into the forebrain, where the protists eat neuronal tissue in the brain, leading to death within 14 days from initial exposure.
• The disease is largely asymptomatic until its final stages; often by the time it is diagnosed, it is too late to treat, causing a very high mortality rate.
• Antimicrobial drugs can combat Naegleria fowleri infection if it is treated soon enough. Avoiding the infection by wearing nose plugs when swimming in warm water is a good preventative measure.
Key Terms
• anosmia: Inability to smell; to perceive odors.
• protist: Any of the eukaryotic unicellular organisms including protozoans, slime molds and some algae; historically grouped into the kingdom Protoctista.
• parosmia: A distorted sense of smell, often resulting in phantom, non-existent, and mostly unpleasant, smells.
• ageusia: Partial or complete loss of the sense of taste.
Primary amoebic meningoencephalitis (PAM, or PAME) is a disease of the central nervous system caused by infection from Naegleria fowleri.
Naegleria fowleri is commonly referred to as an amoeba but is actually a unicellular parasitic protist that is ubiquitous in soils and warm, stagnant bodies of freshwater, especially during the summer months. Patients typically have a history of exposure to a natural body of water.
The organism specifically prefers temperatures above 32 °C, as might be found in a tropical climate or in water heated by geothermal activity. The organism is extremely sensitive to chlorine (<0.5 ppm). Exposure to the organism is extremely common due to its wide distribution in nature.
However, thus far the only route for Naegleria fowleri to enter the central nervous system is via deep insufflation of infected water as it attaches itself to the olfactory nerve, which is exposed only at the extreme vertical terminus of the paranasal sinuses.
When this occurs, it then migrates through the cribiform plate and into the olfactory bulbs of the forebrain, where it multiplies itself greatly by feeding on nerve tissue. During this stage, occurring approximately 3–7 days post-infection, the typical symptoms are parosmia, rapidly progressing to anosmia (with resultant ageusia) as the nerve cells of the olfactory bulbs are consumed and replaced with necrotic lesions.
After the organisms have multiplied and largely consumed the olfactory bulbs, the infection rapidly spreads through the mitral cell axons to the rest of the cerebrum, resulting in onset of frank encephalitic symptoms, including cephalgia (headache), nausea, and rigidity of the neck muscles, progressing to vomiting, delirium, seizures, and eventually irreversible coma. Death usually occurs within 14 days of exposure as a result of respiratory failure when the infection spreads to the brain stem, destroying the autonomic nerve cells of the medulla oblongata.
The disease is both exceptionally rare and highly lethal: there have been fewer than 200 confirmed cases in recorded medical history as of 2004, and 300 cases as of 2008, with an in-hospital case fatality rate of ~97% (3% patient survival rate). Its high mortality rate is largely blamed on the unusually non-suggestive symptomology in its early stages, compounded by the necessity of microbial culture of the cerebrospinal fluid to effect a positive diagnosis. The parasite also demonstrates a particularly rapid late-stage propagation through the nerves of the olfactory system to many parts of the brain simultaneously (including the vulnerable medulla).
Michael Beach, a recreational waterborne-illness specialist for the Centers for Disease Control and Prevention, stated in remarks to the Associated Press that the wearing of nose-clips to prevent nasal uptake of contaminated water would be an effective protection against contracting PAM, noting that, “You’d have to have water going way up in your nose to begin with”.
PAM can be effectively treated with antimicrobiotics, if the patient is treated early enough. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.22%3A_Fungal_Protozoan_Prion_and_Other_Diseases_of_the_Nervous_System/15.22C%3A_Amoebic_Meningoencephalitis.txt |
Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative disease in cows.
Learning Objectives
• Recognize the route of transmission and causes of bovine spongiform encephalopathy (BSE)
Key Points
• BSE is probably caused by a misfolded protein known as a prion; a prion can cause other correctly folded proteins to misfold thus propagating the disease.
• Cooking of prions does not destroy them.
• Evidence exists that when the prions in cows that cause BSE are consumed by humans this causes prion transmission to humans and the neurodegenerative Creutzfeldt-Jakob disease.
Key Terms
• prion: A self-propagating misfolded conformer of a protein that is responsible for a number of diseases that affect the brain and other neural tissue.
• beta sheet: A secondary structure in proteins consisting of multiple strands connected laterally.
• alpha helix: A secondary structure found in many proteins, where the amino acids are arranged in a coil, or helix, with almost no free space on the inside and all side chains being pointed towards the outside.
Bovine spongiform encephalopathy (BSE), commonly known as mad cow disease, is a fatal neurodegenerative disease in cattle that causes a spongy degeneration in the brain and spinal cord. BSE has a long incubation period, about 30 months to eight years, usually affecting adult cattle at a peak age of four to five years, all breeds being equally susceptible.
In the United Kingdom, the country worst affected, more than 180,000 cattle have been infected and 4.4 million slaughtered during the eradication program. The disease may be most easily transmitted to human beings by eating food contaminated with the brain, spinal cord or digestive tract of infected carcasses. However, it should also be noted that the infectious agent, although most highly concentrated in nervous tissue, can be found in virtually all tissues throughout the body, including blood. In humans, it is known as new variant Creutzfeldt–Jakob disease (vCJD or nvCJD), and by October 2009, had killed 166 people in the United Kingdom and 44 elsewhere. Between 460,000 and 482,000 BSE-infected animals had entered the human food chain before controls on high-risk offal were introduced in 1989.
The infectious agent in BSE is believed to be a specific type of misfolded protein called a prion. Prions will not disappear even if the beef containing them is cooked. Prion proteins carry the disease between individuals and cause deterioration of the brain.
BSE is a type of transmissible spongiform encephalopathy (TSE). TSEs can arise in animals that carry an allele which causes previously normal protein molecules to contort by themselves from an alpha helix arrangement to a beta sheet, which is the disease-causing shape for the particular protein. Transmission can occur when healthy animals come in contact with tainted tissues from others with the disease. In the brain, these proteins cause native cellular prion protein to deform into the infectious state, which then goes on to deform further prion protein in an exponential cascade. This results in protein aggregates, which then form dense plaque fibers, leading to the microscopic appearance of “holes” in the brain, degeneration of physical and mental abilities, and ultimately death.
Different hypotheses exist for the origin of prion proteins in cattle. Two leading hypotheses suggest it may have jumped species from the disease scrapie in sheep, or that it evolved from a spontaneous form of “mad cow disease” that has been seen occasionally in cattle for many centuries. In the fifth century BC, Hippocrates described a similar illness in cattle and sheep, which he believed also occurred in man. Publius Flavius Vegetius Renatus recorded cases of a disease with similar characteristics in the fourth and fifth centuries. Recent research suggests mad cow disease is caused by a genetic mutation within a gene called the prion protein gene. The research shows, for the first time, that a 10-year-old cow from Alabama with an atypical form of bovine spongiform encephalopathy had the same type of prion protein gene mutation as found in human patients with the genetic form of Creutzfeldt–Jakob disease, also called genetic CJD, for short. Besides having a genetic origin, other human forms of prion diseases can be sporadic, as in sporadic CJD, as well as foodborne. They are contracted when people eat products contaminated with mad cow disease. This form of Creutzfeldt-Jakob disease is called variant CJD. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.22%3A_Fungal_Protozoan_Prion_and_Other_Diseases_of_the_Nervous_System/15.22D%3A_Bovine_Spongiform_Encephalopathy.txt |
Variant Creutzfeldt–Jakob Disease (vCJD) is a fatal neurological disorder which is caused by prions.
Learning Objectives
• Generalize the role of prions in Creutsfeldt-Jakob disease
Key Points
• Bovine spongiform encephalopathy (BSE) is believed to be the cause of variant Creutzfeldt–Jakob (vCJD); BSE is a prion disease that affects cattle. In both humans and cattle the disease causes large holes in the brain.
• The prion the misfoled protein that causes vCJD has two conformations: one is the native form and is water soluble; the other is the disease form, which is water insoluble.
• The misfolded prion proteins can cause other normally folded pre-prion proteins to become prions, which disrupts the native proteins disrupting function leading to cell death.
• There is no known treatment for vCJD, except avoiding BSE contaminated meat.
Key Terms
• Creutzfeldt–Jakob disease: a rare, progressive, currently fatal disease of the nervous system, characterized by dementia and loss of muscle control; a prion disease, apparently transmissible from animals to humans by eating infected tissue, as well as from tissue interchanges among humans
• prion: A self-propagating misfolded conformer of a protein that is responsible for a number of diseases that affect the brain and other neural tissue.
• transmembrane: traversing a cellular membrane
Creutzfeldt–Jakob disease, or CJD, is a degenerative neurological disorder (brain disease) that is incurable and invariably fatal. CJD is occasionally called a human form of mad cow disease (bovine spongiform encephalopathy or BSE), even though classic CJD is not related to BSE. However, given that BSE is believed to be the cause of variant Creutzfeldt–Jakob disease (vCJD) in humans, the two are often confused. In CJD, the brain tissue develops holes and takes on a sponge-like texture. This is due to a type of infectious protein called a prion. Prions are misfolded proteins which replicate by converting their properly folded counterparts.
Transmissible spongiform encephalopathy diseases are caused by prions. Thus, the diseases are sometimes called prion diseases. Other prion diseases include Gerstmann–Sträussler–Scheinker syndrome (GSS), fatal familial insomnia (FFI) and Kuru in humans; as well as bovine spongiform encephalopathy (BSE, commonly known as mad cow disease) in cattle, chronic wasting disease (CWD) in elk and deer, and Scrapie in sheep. Alpers’ syndrome in infants is also thought to be a transmissible spongiform encephalopathy caused by a prion.
The prion that is believed to cause Creutzfeldt–Jakob exhibits at least two stable conformations. One, the native state, is water-soluble and present in healthy cells. As of 2007, its biological function is presumably in transmembrane transport or signaling. The other conformational state is relatively water-insoluble and readily forms protein aggregates. People can also acquire CJD genetically through a mutation of the gene that codes for the prion protein (PRNP). This occurs in only 5–10% of all CJD cases.
The CJD prion is dangerous because it promotes refolding of native proteins into the diseased state. The number of misfolded protein molecules will increase exponentially and the process leads to a large quantity of insoluble protein in affected cells. This mass of misfolded proteins disrupts cell function and causes cell death. Mutations in the gene for the prion protein can cause a misfolding of the dominantly alpha helical regions into beta pleated sheets. This change in conformation disables the ability of the protein to undergo digestion. Once the prion is transmitted, the defective proteins invade the brain and are produced in a self-sustaining feedback loop. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.22%3A_Fungal_Protozoan_Prion_and_Other_Diseases_of_the_Nervous_System/15.22E%3A_Variant_Creutzfeldt-Jakob_Disease.txt |
Chronic fatigue syndrome (CFS) is the most common persistent fatigue syndrome that affects people.
Learning Objectives
• Recognize the major symptoms associated with chronic fatigue syndrome
Key Points
• CFS is typified by extreme fatigue even in the absence of any type of exertion, and can affect people of all ages.
• There can be many non-fatigue symptoms associated with CFS, with many people exhibiting several different symptoms.
• While no direct association has been shown between a given virus and CFS, the onset of CFS is often preceded with viral infection type symptoms.
Key Terms
• orthostatic: Of, or relating to upright posture.
• morbid: Of, or relating to disease.
• prevalence: the total number of cases of a disease in the given statistical population at a given time, divided by the number of individuals in the population
• encephalomyelitis: Inflammation of the brain and spinal cord.
Chronic fatigue syndrome (CFS) is the most common name used to designate a significantly debilitating medical disorder or group of disorders. Generally defined by persistent fatigue accompanied by other specific symptoms for a minimum of six months in adults (and 3 months in children/adolescents), not due to ongoing exertion, not substantially relieved by rest, and not caused by other medical conditions. The disorder may also be referred to as myalgic encephalomyelitis (ME), post-viral fatigue syndrome (PVFS), chronic fatigue immune dysfunction syndrome (CFIDS), or several other terms.
Biological, genetic, infectious and psychological mechanisms have been proposed for the development and persistence of symptoms but the etiology of CFS is not understood and may have multiple causes. There is no diagnostic laboratory test or biomarker for CFS. Symptoms of CFS include post-exertional malaise; unrefreshing sleep; widespread muscle and joint pain; sore throat; headaches of a type not previously experienced; cognitive difficulties; chronic, often severe, mental and physical exhaustion; and other characteristic symptoms in a previously healthy and active person. Persons with CFS may report additional symptoms such as muscle weakness, increased sensitivity to light, sounds and smells, orthostatic intolerance, digestive disturbances, depression, and cardiac and respiratory problems. It is unclear if these symptoms represent co-morbid conditions or are produced by an underlying etiology of CFS. CFS symptoms vary from person to person in number, type, and severity.
The majority of CFS cases start suddenly, usually accompanied by a “flu-like illness” while a significant proportion of cases begin within several months of severe adverse stress. An Australian prospective study found that after infection by viral and non-viral pathogens, a sub-set of individuals met the criteria for CFS, with the researchers concluding that “post-infective fatigue syndrome is a valid illness model for investigating one pathophysiological pathway to CFS”. However, accurate prevalence and exact roles of infection and stress in the development of CFS are currently unknown.
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The lymphatic system plays a prominent role in immune function, fatty acid absorption, and removal of interstitial fluid from tissues.
Learning Objectives
• Describe the roles of the lymphatic system
Key Points
• The lymphatic system is a linear network of lymphatic vessels and secondary lymphoid organs. It is the site of many immune system functions as well as its own functions.
• It is responsible for the removal of interstitial fluid from tissues into lymph fluid, which is filtered and brought back into the bloodstream through the subclavian veins near the heart.
• Edema accumulates in tissues during inflammation or when lymph drainage is impaired.
• It absorbs and transports fatty acids and fats as chylomicrons from the digestive system.
• It transports white blood cells and dendritic cells to lymph nodes where adaptive immune responses are often triggered.
• Tumors can spread through lymphatic transport.
Key Terms
• lacteal: A lymphatic capillary that absorbs dietary fats in the villi of the small intestine.
• interstitial fluid: Also called tissue fluid, a solution that bathes and surrounds the cells of multicellular animals.
• white blood cell: A type of blood cell involved with an immune response. Many white blood cells (primarily lymphocytes) are transported by the lymphatic system.
The lymphatic system is the site of many key immune system functions. It is important to distinguish that immune system functions can happen almost anywhere in the body, while the lymphatic system is its own system where many immune system functions take place. Besides immune system function, the lymphatic system has many functions of its own. It is responsible for the removal and filtration of interstitial fluid from tissues, absorbs and transports fatty acids and fats as chyle from the digestive system, and transports many of the cells involved in immune system function via lymph.
Removal of Fluid
Interstitial fluid accumulates in the tissues, generally as a result of the pressure exerted from capillaries (hydrostatic and osmotic pressure) or from protein leakage into the tissues (which occurs during inflammation). These conditions force fluid from the capillaries into the tissues. One of the main functions of the lymphatic system is to drain the excess interstitial fluid that accumulates.
The lymphatic system is a blunt-ended linear flow system, in which tissue fluids, cells, and large extracellular molecules, collectively called lymph, are drained into the initial lymphatic capillary vessels that begin at the interstitial spaces of tissues and organs. They are then transported to thicker collecting lymphatics, which are embedded with multiple lymph nodes, and are eventually returned to the blood circulation through the left and right subclavian veins and into the vena cava. They drain into venous circulation because there is lower blood pressure in veins, which minimizes the impact of lymph cycling on blood pressure. Lymph nodes located at junctions between the lymph vessels also filter the lymph fluid to remove pathogens and other abnormalities.
Fluid removal from tissues prevents the development of edema. Edema is any type of tissue swelling from increased flow of interstitial fluid into tissues relative to fluid drainage. While edema is a normal component of the inflammation process, in some cases it can be very harmful. Cerebral and pulmonary edema are especially problematic, which is why lymph drainage is so important. Abnormal edema can still occur if the drainage components of the lymph vessels are obstructed.
Fatty Acid Transport
The lymphatic system also facilitates fatty acid absorption from the digestive system. During fat digestion, fatty acids are digested, emulsified, and converted within intestinal cells into a lipoprotein called chylomicrons. Lymph drainage vessels that line the intestine, called lacteals, absorb the chylomicrons into lymph fluid. The lymph vessels then take the chylomicrons into blood circulation, where they react with HDL cholesterols and are then broken down in the liver.
Immune Cell Transport
In addition to tissue fluid homeostasis, the lymphatic system serves as a conduit for transport of cells involved in immune system function. Most notably, highly-specialized white blood cells called lymphocytes and antigen -presenting cells are transported to regional lymph nodes, where the immune system encounters pathogens, microbes, and other immune elicitors that are filtered from the lymph fluid. Much of the adaptive immune system response, which is mediated by dendritic cells, takes place in the lymph nodes. Lymphatic vessels, which uptake various antigens from peripheral tissues, are positively regulated by chemokines/cytokines secreted by various immune cells during inflammation. This allows antigens to enter lymph nodes, where dendritic cells can present them to lymphocytes to trigger an adaptive immune response.
While the lymphatic system is important for transporting immune cells, its transport capabilities can also provide a pathway for the spread of cancer. Lymph circulation is one of the main ways that tumors can spread to distant parts of the body, which is difficult to prevent. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.23%3A_Microbial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.23A%3A_Functions_of_the_Lymphatic_System.txt |
Both the cardiovascular system and the lymphatic system are susceptible to diseases caused by microorganisms.
Learning Objectives
• Compare and contrast the causes associated with: endocarditis, myocarditis, bacteremia, vasculitis and lymphatic disease
Key Points
• Two common cardiovascular diseases caused by infection with microorganisms are endocarditis and myocarditis.
• Endocarditis is inflammation of the inner tissue of the heart such as its valves caused by infectious agents.
• Myocarditis is inflammation of heart muscle and it is most often due to infection by common viruses.
• Bacteremia is the presence of bacteria in the blood.
• Vasculitis is inflammation of the vessel wall due to an infection or autoimmune disease.
• Lymphadenopathy is a disease of the lymph nodes due to infection, auto- immune disease, or malignancy.
Key Terms
• Endocarditis: An inflammation of the endocardium and possibly the heart valves.
• myocarditis: Inflammation of the myocardium.
• lymphadenopathy: An abnormal enlargement of the lymph nodes
• Vasculitis: Inflammation of the vessel wall due to an infection or autoimmune disease.
• bacteremia: The presence of bacteria in the blood.
Both the cardiovascular system and the lymphatic system are susceptible to diseases caused by microorganisms.
In the cardiovascular system, the heart, the blood vessels (arteries, capillaries, and veins), and the blood are targets of pathogens. Two common cardiovascular diseases caused by infection with microorganisms are endocarditis and myocarditis.
1. Endocarditis is inflammation of the inner tissue of the heart such as its valves caused by infectious agents. The agents are usually bacterial, but other organisms can also be responsible. Since, the valves of the heart do not receive any dedicated blood supply, the defensive immune mechanisms (such as white blood cells) cannot directly reach the valves via the bloodstream. The lack of blood supply to the valves also has implications for treatment, since drugs also have difficulty reaching the infected valve.
2. Myocarditis or inflammatory cardiomyopathy is inflammation of heart muscle (myocardium) and it is most often due to infection by common viruses, such as parvovirus B19. It is often caused by an autoimmune reaction. Streptococcal M protein and coxsackievirus B have regions (epitopes) that are immunologically similar to cardiac myosin. During and after the viral infection, the immune system may attack cardiac myosin. Because a definitive diagnosis requires a heart biopsy, which doctors are reluctant to do because they are invasive, statistics on the incidence of myocarditis vary widely. The consequences of myocarditis thus also vary widely. It can cause a mild disease without any symptoms that resolves itself, or it may cause chest pain, heart failure, or sudden death. As most viral infections cannot be treated with directed therapy, symptomatic treatment is the only form of therapy for those forms of myocarditis. In the acute phase, supportive therapy, including bed rest, is indicated. For symptomatic patients, digoxin and diuretics provide clinical improvement.
Bacteremia is the presence of bacteria in the blood. Bacteria can enter the bloodstream as a severe complication of infections (like pneumonia or meningitis), during surgery (especially when involving mucous membranes such as the gastrointestinal tract), or due to catheters and other foreign bodies entering the arteries or veins (including intravenous drug abuse). Bacteremia can have several consequences. The immune response to the bacteria can cause sepsis and septic shock, which has a relatively high mortality rate. Bacteria can also use the blood to spread to other parts of the body (which is called hematogenous spread), causing infections away from the original site of infection. Examples include endocarditis or osteomyelitis. Treatment is with antibiotics, and prevention with antibiotic prophylaxis can be given in situations where problems are to be expected.
Vasculitis is inflammation of the vessel wall due to an infection (or autoimmune disease). Blood vessel permeability is increased in inflammation. Damage, due to trauma or spontaneously, may lead to hemorrhage due to mechanical damage to the vessel endothelium.
Lymphatic disease is a class of disorders that directly affect the components of the lymphatic system. Lymphadenopathy is a term meaning disease of the lymph nodes due to infection, auto-immune disease, or malignancy. Enlarged lymph nodes are a common symptom in a number of infectious diseases, of which some are as follows:
1. Acute infection (e.g., bacterial, or viral), or chronic infections (tuberculous lymphadenitis, cat-scratch disease).
2. The most distinctive symptom of bubonic plague is extreme swelling of one or more lymph nodes that bulge out of the skin as “buboes. ” The buboes often become necrotic and may even rupture.
3. Infectious mononucleosis is an acute viral infection, the hallmark of which is marked enlargement of the cervical lymph nodes.
4. It is also a symptom of cutaneous anthrax, measles and Human African trypanosomiasis, the latter two giving lymphadenopathy in lymph nodes in the neck.
5. Toxoplasmosis, a parasitic disease, gives a generalized lymphadenopathy. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.23%3A_Microbial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.23B%3A_The_Cardiovascular_System.txt |
The lymphatic system consists of lymphatic vessels and associated lymphoid organs.
Learning Objectives
• Describe the structure and function of the lymphatic system
Key Points
• The lymphatic system is a circulatory system that drains fluid from the blood vessels.
• Lymph vessels are the site of fluid drainage and pump lymph fluid using smooth muscle and skeletal muscle action. The larger vessels contain valves to prevent backflow and pump towards the heart to return lymph fluid to the bloodstream by the subclavian veins.
• A lymph node is an organized collection of lymphoid tissue through which the lymph passes on its way to returning to the blood. Lymph nodes are located at intervals along the lymphatic system.
• Lymphoid tissue contains lymphocytes and other specialized cells and tissues that have immune system functions.
Key Terms
• lymph node: Small oval bodies of the lymphatic system, distributed along the lymphatic vessels clustered in the armpits, groin, neck, chest, and abdomen. They filter through lymph fluid.
• lymph: A colorless, watery, bodily fluid carried by the lymphatic system, consisting mainly of white blood cells.
The lymphatic system is a collection of structures and vessels that drains lymph from blood and has several other functions. It is a circulatory system for lymph fluid and the site of many key immune system functions.
Lymphatic Vessels
The lymphatic vessels are the lymphatic system equivalent of the blood vessels of the circulatory system and drain fluid from the circulatory system. The network of lymph vessels consists of the initial collectors of lymph fluid, which are small, valveless vessels, and goes on to form the precollector vessels, which have rudimentary valves that are not fully functional. These structures then form increasingly larger lymphatic vessels which form colaterals and have lymph-angions (lymph hearts). The larger lymph vessels contain valves that prevent the backflow of lymph.
The lymphatic system is an active pumping system driven by segments that have a function similar to peristalsis. They lack a central pump (like the heart in the cardio vascular system), so smooth muscle tissue contracts to move lymph along through the vessels. Skeletal muscle contractions also move lymph through the vessels. The lymphatic vessels make their way to the lymph nodes, and from there the vessels form into trunks. In general, the lymph vessels bring lymph fluid toward the heart and above it to the subclavian veins, which enable lymph fluid to re-enter the circulatory system through the vena cava.
Lymphatic Tissues and Organs
Lymphoid tissue is found in many organs including the lymph nodes, as well as in the lymphoid follicles in the pharynx such as the tonsils. Lymph nodes are found primarily in the armpits, groin, chest, neck, and abdomen. Lymphoid tissues contain lymphocytes (a type of highly differentiated white blood cell), but they also contain other types of cells for structural and functional support, such as the dendritic cells, which play a key role in the immune system. The system also includes all the structures dedicated to the circulation and production of lymphocytes, including the spleen, thymus, and bone marrow. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.23%3A_Microbial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.23C%3A_Structure_of_the_Lymphatic_System.txt |
The circulatory system has a defence against microbial invaders in the form of the lymphatic system.
Learning Objectives
• Summarize the role of the lymphatic system during an infection
Key Points
• The lymphatic system works in close cooperation with other body systems to destroy pathogens and filter waste.
• The lymphatic system contains immune cells called lymphocytes, which protect the body against antigens (viruses, bacteria, etc. ) that invade the body. Lymph nodes are sites of both microbial destruction and the production of antibodies against other foreign invaders.
• While the lymph system acts as a defence against microbial invaders it can also cause problems. Notably over-swelling, and acting as a home for bacterial invaders, even spreading bacteria or cancerous cells.
• Lymph is the fluid that is formed when interstitial fluid enters the initial lymphatic vessels of the lymphatic system and transports antigen-presenting cells (APCs), such as dendritic cells, to the lymph nodes where an immune response is stimulated.
Key Terms
• lymphatic system: In mammals, including humans, a network of lymph vessels and lymph nodes that transport fluid, fats, proteins, and lymphocytes to the bloodstream as lymph, and remove microorganisms and other debris from tissues.
• lymphocytes: type of white blood cells in the vertebrate immune system
The cardiovascular and lymphatic are both integral parts of the circulatory system. The cardiovascular system basically moves blood throughout the body. While the lymphatic system is part of the circulatory system, comprising a network of conduits called lymphatic vessels. Rather than blood the lymph systems carries a clear fluid called lymph (from Latin lympha, meaning “water goddess”) unidirectionally towards the heart. The lymph system is not a closed system. The circulatory system processes an average of 20 liters of blood per day through capillary filtration which removes plasma while leaving the blood cells. While the circulatory system is essential for survival, it also is the source of a major problem when dealing with microbial infections. Many microbes take advantage of the circulatory system to spread throughout the body. Not surprising then the lymphatic system is critical for the bodies immune response to microbial infections. Lymphatic organs play an important part in the immune system, having a considerable overlap with the lymphoid system. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. Lymphoid tissues contain lymphocytes, but they also contain other types of cells for support. The system also includes all the structures dedicated to the circulation and production of lymphocytes (the primary cellular component of lymph), which includes the spleen, thymus, bone marrow, and the lymphoid tissue associated with the digestive system.
As well as filtering the lymph, lymph nodes produce the white cells known as lymphocytes. Lymphocytes are also produced by the thymus, spleen and bone marrow. There are two kinds of lymphocyte. The first attach invading micro organisms directly while others produce antibodies that circulate in the blood and attack them. When micro-organisms invade the body, or the body encounters antigens (such as pollen), antigens are transported to the lymph. Lymph is carried through the lymph vessels to regional lymph nodes. In the lymph nodes, the macrophages and dendritic cells phagocytose the antigens, process them, and present the antigens to lymphocytes, which can then start producing antibodies or serve as memory cells. The function of memory cells is to recognize specific antigens in the future. The function of the lymphatic system can therefore be summarized as transport and defense. It is important for returning the fluid and proteins that have escaped from the blood capillaries to the blood system and is also responsible for picking up the products of fat digestion in the small intestine. Its other essential function is as part of the immune system, defending the body against infection.
While the lymph nodes do battle infections, there are problems with lymph nodes and the lymphatic system. During infection of the body the lymph nodes often become swollen and tender because of their increased activity. This is what causes the swollen ‘glands’ in your neck during throat infections, mumps and tonsillitis. Sometimes the bacteria multiply in the lymph node and cause inflammation. Cancer cells may also be carried to the lymph nodes and then transported to other parts of the body where they may multiply to form a secondary growth or metastasis. The lymphatic system may therefore contribute to the spread of cancer. Inactivity of the muscles surrounding the lymphatic vessels or blockage of these vessels causes tissue fluid to ‘back up’ in the tissues resulting in swelling or edema.
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Septic shock occurs when a body’s response to an infection (sepsis) leads to life-threatening low blood pressure.
Learning Objectives
• Compare and contrast the symptoms of: sepsis, severe sepsis, septic shock
Key Points
• Sepsis results from certain bacterial infections, often acquired in a hospital. Having certain conditions, such as a weakened immune system, certain chronic disorders, an artificial joint, or heart valve increases the risk.
• Symptoms of sepsis include either fever or low body temperature, rapid breathing, chills and shaking, rapid heartbeat, decreased urine output, and confusion or delirium.
• Severe sepsis often causes extremely low blood pressure, which limits blood flow to the body and can result in organ failure and death. This is known as septic shock.
• Sepsis is treated with antibiotics, fluids, and medicines to support blood pressure and prevent organ damage.
Key Terms
• septic shock: A life-threatening condition caused by infection and sepsis, often after surgery or trauma.
• sepsis: A life-threatening medical condition caused by a severe inflammatory response of the human body triggered by the presence of an infectious agent.
• mortality rate: the number of deaths per given unit of population over a given period of time
Sepsis is a potentially deadly medical condition characterized by a whole-body inflammatory state (called a systemic inflammatory response syndrome or SIRS) that is triggered by an infection. Septic shock is a medical condition as a result of severe infection and sepsis, though the microbe may be systemic or localized to a particular site. Its most common victims are children, immuno-compromised individuals, and the elderly, as their immune systems cannot deal with the infection as effectively as those of healthy adults. Frequently, patients suffering from septic shock are cared for in intensive care units. The mortality rate from septic shock is approximately 25–50%.
Sepsis
Sepsis is an illness in which the body has a severe response to bacteria or other germs. The body may develop this inflammatory response by the immune system to microbes in the blood, urine, lungs, skin, or other tissues. A popular term for sepsis is blood poisoning. Severe sepsis is the systemic inflammatory response, infection, and the presence of organ dysfunction.
A bacterial infection anywhere in the body may set off the response that leads to sepsis. Common places where an infection might start include:
• the bloodstream
• bones (common in children)
• the bowel (usually seen with peritonitis)
• the kidneys (upper urinary tract infection or pyelonephritis )
• the lining of the brain ( meningitis )
• the liver or gallbladder
• the lungs (bacterial pneumonia )
• the skin (cellulitis)
For patients in the hospital, common sites of infection include intravenous lines, surgical wounds, surgical drains, and sites of skin breakdown known as bedsores (decubitus ulcers).
The therapy of sepsis rests on intravenous fluids, antibiotics, surgical drainage of infected fluid collections, and appropriate support for organ dysfunction. This may include hemodialysis in kidney failure, mechanical ventilation in pulmonary dysfunction, transfusion of blood products, and drug and fluid therapy for circulatory failure. Ensuring adequate nutrition—preferably by enteral feeding, but if necessary by parenteral nutrition—is important during prolonged illness.
Septic Shock
In sepsis, blood pressure drops, resulting in septic shock. Major organs and body systems, including the kidneys, liver, lungs, and central nervous system, stop working properly because of poor blood flow.
Most cases of septic shock are caused by Gram-positive bacteria, followed by endotoxin-producing Gram-negative bacteria. Endotoxins are bacterial membrane lipopolysaccharides (LPS) consisting of a toxic fatty acid (lipid A) core common to all Gram-negative bacteria, and a complex polysaccharide coat (including O antigen) unique for each species. Analogous molecules in the walls of Gram-positive bacteria and fungi can also elicit septic shock. In Gram-negative sepsis, free LPS attaches to a circulating LPS-binding protein, and the complex then binds to a specific receptor (CD14) on monocytes, macrophages, and neutrophils.
If sepsis worsens to the point of end-organ dysfunction (renal failure, liver dysfunction, altered mental status, or heart damage) then the condition is called severe sepsis. Once severe sepsis worsens to the point where blood pressure can no longer be maintained with intravenous fluids alone, then the criteria have been met for septic shock. The precipitating infections which may lead to septic shock if severe enough include appendicitis, pneumonia, bacteremia, diverticulitis, pyelonephritis, meningitis, pancreatitis, and necrotizing fasciitis.
Treatment primarily consists of the following:
1. Volume resuscitation
2. Early antibiotic administration
3. Early goal directed thearpy
4. Rapid source identification and control.
5. Support of major organ dysfunction.
There are new drugs that act against the extreme inflammatory response seen in septic shock. These may help limit organ damage.
The mortality rate from sepsis is approximately 40% in adults, and 25% in children, and is significantly greater when left untreated for more than seven days. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.24%3A_Bacterial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.24A%3A_Sepsis_and_Septic_Shock.txt |
Bacterial endocarditis is an infection of the inner surface of the heart or heart valves caused by the presence of bacteria in the blood.
Learning Objectives
• Recognize the causes and treatments for endocarditis
Key Points
• Endocarditis occurs when bacteria grow on the edges of a heart defect or on the surface of an abnormal valve after the bacteria enter the blood stream, most commonly from dental procedures but also from procedures involving the gastrointestinal or urinary tract.
• The most important diagnostic test for endocarditis involves a positive blood culture. A blood culture is a small sample of blood drawn from the vein which is grown in a special solution so that bacteria can be detected.
• Symptoms and signs of endocarditis vary but include prolonged fever poor appetite, feeling weak or tired, joint pains, skin rashes, and changes in the nature of a previously present heart murmur.
• Treatment of bacterial endocarditis consists of a period of intravenous doses of appropriate antibiotics determined from blood tests under the supervision of an infectious disease specialist and cardiologist.
Key Terms
• Endocarditis: An inflammation of the interior lining of the heart or the endocardium and possibly the heart valves (pathology, cardiology).
• bacteremia: The medical condition of having bacteria in the bloodstream.
In a healthy individual, a bacteremia (where bacteria get into the blood stream through a minor cut or wound) would normally be cleared quickly with no adverse consequences. If a heart valve is damaged and covered with a piece of blood clot, the valve provides a place for the bacteria to attach themselves and an infection can be established. Endocarditis, or inflammation of the inner tissue of the heart, occurs as a result. The valves of the heart do not receive any dedicated blood supply. As a result, defensive immune mechanisms (such as white blood cells) cannot directly reach the valves via the bloodstream. When bacteria attaches to a valve surface and forms a vegetation, the host immune response is blunted. The lack of blood supply to the valves also has implications for treatment, since drugs also have difficulty reaching the infected valve. Normally, blood flows smoothly through these valves. If they have been damaged – from rheumatic fever, for example – the risk of bacterial attachment is increased.
Bacteremia caused by dental procedures (in most cases due to streptococci viridans, which reside in oral cavity), such as a cleaning or extraction of a tooth and from procedures involving the gastrointestinal or urinary tract can cause bacterial endocarditis. Intravenous drug abuse may also cause bacterial endocarditis from the aseptic introduction of skin bacteria.
Symptoms and signs of endocarditis vary, but prolonged fever (more then 2-3 days) without an obvious cause is a most important sign and should always be investigated in a child with congenital heart disease. Other signs and symptoms include poor appetite, feeling weak or tired, joint pains, skin rashes, and changes in the nature of a previously present heart murmur. The chance that these signs and symptoms are caused by endocarditis is more likely if they occur soon after a dental cleaning or procedure involving the gastrointestinal or urinary tract.
High dose antibiotics are administered by the intravenous route to maximize diffusion of antibiotic molecules into vegetation(s) from the blood filling the chambers of the heart. This is necessary because neither the heart valves nor the vegetations adherent to them are supplied by blood vessels. Antibiotics are continued for a long time, typically two to six weeks depending on the characteristics of the infection and the causative microorganisms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.24%3A_Bacterial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.24B%3A_Bacterial_Infections_of_the_Heart.txt |
Rheumatic fever is an inflammatory disease that can develop as a complication of inadequately treated strep throat.
Learning Objectives
• Outline the effect of infection by Steptococcus pyogenes on the immune system
Key Points
• Rheumatic fever is a condition that is a complication of untreated strep throat. Strep throat is caused by a group A streptococcal infection found in the throat.
• When the body senses the strep infection, it sends antibodies to fight it and sometimes these antibodies attack the tissues of your joints or heart instead. This is known as anitbody cross-reactivity which leads to rheumatic fever.
• Symptoms of rheumatic fever occur several weeks after initial throat problems have disappeared; and include chest pain, fever, heart problems, joint pain, nosebleeds, and skin rash.
• Rheumatic fever is treated using a combination of antibiotics and anti-inflammatory medications.
Key Terms
• rheumatism: Any disorder of the muscles, tendons, joints, bones, nerves, characterized by pain, discomfort and disability.
• Streptococcus: A spherical, gram-positive bacterium of the genus Streptococcus. Although commonly found benignly in the human mouth and gut, and though many species are non-pathogenic, other species can cause diseases including strep throat and more serious conditions.
Rheumatic fever is an inflammatory disease that occurs following a Streptococcus pyogenes infection, such as streptococcal pharyngitis (strep throat) or scarlet fever, that affects the peri-arteriolar connective tissue. Believed to be caused by antibody cross-reactivity that can involve the heart, joints, skin, and brain; the illness typically develops two to three weeks after a streptococcal infection.
Acute rheumatic fever commonly appears in children between the ages of six and 15, with only 20% of first-time attacks occurring in adults. The illness is so named because of its similarity in presentation to rheumatism.
This cross-reactivity is a Type II hypersensitivity reaction and is termed molecular mimicry. During a Streptococcus infection, mature antigen -presenting cells, such as B cells, present the bacterial antigen to CD4-T cells which differentiate into helper T2cells. In turn, Helper T2 cells activate the B cells to become plasma cells and induce the production of antibodies against the cell wall of Streptococcus. However the antibodies may also react against the myocardium and joints, producing the symptoms of rheumatic fever.
Diagnosis of rheumatic fever can be made when two of the major criteria, or one major plus two minor criteria, are present along with evidence of streptococcal infection.
The major criteria for diagnosis include:
• Arthritis in several large joints (polyarthritis)
• Heart inflammation (carditis)
• Nodules under the skin (subcutaneous skin nodules)
• Rapid, jerky movements (chorea, Sydenham chorea)
• Skin rash (erythema marginatum)
Minor Criteria:
• Fever of 38.2–38.9 °C (101–102 F)
• Arthralgia: Joint pain without swelling (Cannot be included if polyarthritis is present as a major symptom)
• Raised erythrocyte sedimentation rate or C reactive protein
• Leukocytosis
• ECG showing features of heart block, such as a prolonged PR interval (Cannot be included if carditis is present as a major symptom)
• Previous episode of rheumatic fever or inactive heart disease.
Acute rheumatic fever is treated with antibiotics and anti-inflammatory medications such as aspirin and corticosteroids. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.24%3A_Bacterial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.24C%3A_Rheumatic_Fever.txt |
Tularemia is an infection caused by the Gram-negative bacteria Francisella tularensis.
Learning Objectives
• Recall the mode of transmission and symptoms associated with tularemia
Key Points
• Tularemia is an infection common in wild rodents that is passed to humans through contact with infected animal tissues or by ticks, biting flies, and mosquitoes.
• Symptoms vary depending upon the site of infection. The main clinical signs include fever, lethargy, anorexia, muscle pains and signs of septicemia.
• Although tularemia can be life-threatening, most infections can be treated successfully with antibiotics.
Key Terms
• Francisella tularensis: Francisella tularensis is a pathogenic species of gram-negative bacteria and the causative agent of tularemia or rabbit fever.
• macrophage: A white blood cell that phagocytizes necrotic cell debris and foreign material, including viruses, bacteria, and tattoo ink. It presents foreign antigens on MHC II to lymphocytes. Part of the innate immune system.
• tularemia: An infectious disease caused by the bacterium Francisella tularensis.
Tularemia (also known as Pahvant Valley plague, rabbit fever, deer fly fever, and Ohara’s fever) is a serious infectious disease caused by the bacterium Francisella tularensis. A Gram-negative, nonmotile coccobacillus, the bacterium has several subspecies with varying degrees of virulence.
The most important of these is F. tularensis tularensis (Type A), which is found in lagomorphs (rabbits and similar animals) in North America, and it is highly virulent in humans and domestic rabbits. F. tularensis palaearctica (Type B) occurs mainly in aquatic rodents (beavers, muskrats) in North America and in hares and small rodents in northern Eurasia. It is less virulent for humans and rabbits.
The primary vectors are ticks and deer flies, but the disease can also be spread through other arthropods. The disease is named after Tulare County, California and most commonly occurs in North America and parts of Europe and Asia. Although outbreaks can occur in the United States, they are rare.
Depending on the site of infection, tularemia has six characteristic clinical symptoms: ulceroglandular, glandular, oropharyngeal, pneumonic, oculoglandular, and typhoidal. The incubation period for tularemia is one to 14 days; most human infections become apparent after three to five days.
In most susceptible mammals, the clinical signs include fever, lethargy, anorexia, signs of septicemia, and possibly, death. Fever is moderate or very high. Tularemia bacilli can be isolated from blood cultures at this stage. The face and eyes redden and become inflamed. Inflammation spreads to the lymph nodes, which enlarge and may suppurate (mimicking bubonic plague), accompanied by a high fever. Death occurs in less than 1% if therapy is initiated promptly.
Francisella tularensis is an intracellular bacterium, meaning it is able to live as a parasite within host cells. It primarily infects macrophages and is able to evade the immune system. The course of disease involves the spread of the organism to multiple organ systems, including the lungs, liver, spleen, and lymphatic system; and differs according to the route of exposure.
Tularemia is primarily treated with streptomycin but can also be treated with gentamicin for ten days and tetracycline-class drugs such as doxycycline for two to three weeks, chloramphenicol, or fluoroquinolones. An attenuated, live vaccine is available, but its use is only for high-risk groups.
15.24E: Brucellosis (Undulant Fever)
Brucellosis is an infectious disease that occurs from contact with animals carrying Brucella bacteria.
Learning Objectives
• Recognize the causes and symptoms of brucellosis
Key Points
• Brucella can infect cattle, goats, dogs, and pigs. The bacteria can spread to humans by ingesting unsterilized milk or meat from infected animals, or close contact with their secretions.
• Brucellosis symptoms include fever, joint pain and fatigue. The infection can usually be treated successfully with antibiotics.
• People working in jobs where they often come in contact with animals or meat such as slaughterhouse workers, farmers, and veterinarians are at higher risk for contracting Brucellosis.
Key Terms
• brucellosis: Disease caused by the bacterium, Brucella, which is carried by ruminants. Symptoms include recurring fevers, sweating, weakness, anorexia, headaches, depression and generalized aches and pains.
• Brucella: A genus of Gram-negative bacteria. They are small, non-motile, non-encapsulated coccobacilli, which function as facultative intracellular parasites.
Brucellosis, also called Bang’s disease, Crimean fever, Gibraltar fever, Malta fever, Maltese fever, Mediterranean fever, rock fever, or undulant fever, is a highly-contagious zoonosis caused by ingestion of unsterilized milk or meat from infected animals or close contact with their secretions. Transmission from human to human, through sexual contact or from mother to child, is rare but possible.
Brucella spp. are small, gram-negative, non-motile, non-spore-forming, rod-shaped (coccobacilli) bacteria. They function as facultative intracellular parasites causing chronic disease, which usually persists for life. Symptoms include profuse sweating, and joint and muscle pain.
Species infecting domestic livestock are B. melitensis (goats and sheep), B. suis (pigs), B. abortus (cattle), B. ovis (sheep), and B. canis (dogs). B. abortus also infects bison and elk in North America and B. suis is endemic in caribou. Brucella species have also been isolated from several marine mammal species (pinnipeds and cetaceans).
Brucellosis in humans is usually associated with the consumption of unpasteurized milk and soft cheeses made from the milk of infected animals, primarily goats, infected with Brucella melitensis, as well as with occupational exposure of laboratory workers, veterinarians, and slaughterhouse workers. Some vaccines used in livestock, most notably B. abortus strain 19, also cause disease in humans if accidentally injected.
Brucellosis induces inconstant fevers, sweating, weakness, anaemia, headaches, depression, and muscular and bodily pain. The symptoms are like those associated with many other febrile diseases, but with emphasis on muscular pain and sweating.
The duration of the disease can vary from a few weeks to many months or even years. In the first stage of the disease, septicemia occurs and leads to the classic triad of undulant fevers, sweating (often with characteristic smell, likened to wet hay), and migratory arthralgia and myalgia.
Antibiotics like tetracyclines, rifampicin, and the aminoglycosides streptomycin and gentamicin are effective against Brucella bacteria. However, the use of more than one antibiotic is needed for several weeks, because the bacteria incubate within cells. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.24%3A_Bacterial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.24D%3A_Tularemia.txt |
Anthrax is a rare, infectious disease caused by Bacillus anthracis that can spread from animals to humans.
Learning Objectives
• Discuss the causes and mode of transmission for anthrax including: inhalation, ingestion and direct entry through abrasions
Key Points
• Bacillus anthracis exists in the soil as spores. Spores are inactive forms of the bacteria and can survive for decades in this form.
• Humans can become infected through contact with the anthrax spores from infected animals. It is not conatgious and cannot be spread from one infected person to another person.
• There are three ways one can become infected with anthrax: by inhalation of anthrax spores, entrance of spores through cuts in the skin, and by eating undercooked meat containing anthrax spores.
• Anthrax can be successfully treated with early antibiotic treatment. An anthrax vaccine has been approved for use in humans and is effective in protecting against an anthrax infection.
Key Terms
• Bacillus anthracis: Bacillus anthracis is the etiologic agent of anthrax and the only obligate pathogen within the genus Bacillus. B. anthrais a Gram-positive, endospore-forming, rod-shaped bacterium, with a width of 1-1.2µm and a length of 3-5µm.It can be grown in an ordinary nutrient medium under aerobic or anaerobic conditions.
• anthrax: An infectious bacterial disease of herbivores than can also occur in humans through contact with infected animals, tissue from infected animals, or high concentrations of anthrax spores.
Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and animals. Anthrax commonly infects wild and domesticated herbivorous mammals that ingest or inhale the spores while grazing. Carnivores living in the same environment may become infected by consuming infected animals. Humans become infected through contact with the anthrax spores from infected animals.
Bacillus anthracis is a rod-shaped, Gram-positive, aerobic bacterium about 1 by 9 micrometers in length. The bacterium normally rests in endospore form in the soil, and can survive for decades in this state. B.anthracis bacterial spores have been known to have reinfected animals over 70 years after burial sites of anthrax-infected animals were disturbed. Herbivores are often infected whilst grazing or browsing, especially when eating rough, irritant, or spiky vegetation. It has been hypothesized that the vegetation may cause wounds within the gastrointestinal tract, permitting entry of the bacterial endospores into the tissues. This has not been proven, however. Once ingested or placed in an open wound, the bacterium begins multiplying inside the animal or human and typically kills the host within a few days or weeks. The endospores germinate at the site of entry into the tissues and then spread via the circulation to the lymphatics, where the bacteria multiply.
There are three ways in which people can become infected by anthrax:
1. By inhaling contaminated air containing anthrax spores. This is known as inhalation anthrax or pulmonary anthrax and can cause serious, sometimes lethal respiratory disease. Symptoms are flu-like, but soon develop into nausea and severe breathing problems. Inhalation anthrax has a 97% mortality rate.
2. By handling infected animals and/or animal products, antrax spores can enter through cuts in the skin. This is known as cutaneous anthrax. It first appears as a boil-like lesion then eventually forms a painless ulcer with a black center. Death is rare when the appropriate antibiotics are used.
3. By eating undercooked meat containing anthrax spores. This is known as gastrointestinal antrax. This is rare, with only 2 cases reported in the United States. Symptoms include intestinal inflammation, nausea, loss of appetite, vomiting of blood, abdominal pain and severe diarrhea.
Anthrax can be treated with anitbiotics. The earlier the anthrax is treated, the higher the chance of survival. Treatment for anthrax infection and other bacterial infections includes large doses of intravenous and oral antibiotics, such as fluoroquinolones (like ciprofloxacin), doxycycline, erythromycin, vancomycin, or penicillin. FDA-approved agents include ciprofloxacin, doxycycline, and penicillin. In possible cases of inhalation anthrax, early antibiotic prophylaxis treatment is crucial to prevent possible death.
In the United States, the human anthrax vaccine is required for most US military units and civilian contractors assigned to homeland bioterrorism defense or deployed in Iraq, Afghanistan or South Korea. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.24%3A_Bacterial_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.24F%3A_Anthrax.txt |
Gangrene is a serious and potentially life-threatening condition that arises when a considerable mass of body tissue dies.
Learning Objectives
• Compare and contrast the different types of gangrene: dry, wet, gas, noma, fournier gangrene and necrotizing fasciitis
Key Points
• Gangrene may be caused by an infection, injury, or a complication of a long-term condition that restricts blood circulation.
• There are six main types of gangrene: dry gangrene, wet gangrene. gas gangrene, necrotizing fasciitis, Fournier’s gangrene, and noma.
• Dead tissue cannot be saved, and amputation is necessary in most cases.
Key Terms
• gangrene: The death of tissue due to reduced blood supply as a result of infection or a blocked blood vessel.
• necrosis: The localized death of cells or tissues through injury, disease, or the interruption of blood supply.
• debridement: The removal of dead, damaged, or infected tissue to improve the healing potential of the remaining healthy tissue.
Gangrene is a serious and potentially life-threatening condition that arises when a considerable mass of body tissue dies. This may occur after an injury or infection, or in people suffering from chronic health problems affecting blood circulation. The primary cause of gangrene is reduced blood supply to the affected tissues, which results in necrosis, or cell death. Diabetes and long-term smoking increase the risk of suffering from gangrene.
There are different types of gangrene with different symptoms, including:
• Dry gangrene begins at the distal part of a limb due to ischemia (restriction of circulation), and often occurs in the toes and feet of elderly patients due to arteriosclerosis (hardening of the arteries). Dry gangrene spreads slowly until it reaches the point where the blood supply is adequate to keep tissue viable. The affected part is dry, shrunken, and dark reddish-black, resembling mummified flesh. The gangrenous tissue most often detaches spontaneously.
• Wet gangrene occurs in naturally moist tissue and organs such as the mouth, bowel, lungs, cervix, and vulva. Bedsores occurring on body parts such as the sacrum, buttocks, and heels are also categorized as wet gangrene infections. In wet gangrene, the tissue is infected by microorganisms that cause decay, in turn causing tissue to swell and emit a fetid smell. Wet gangrene usually develops rapidly due to blockage of blood flow, most commonly in veins. The affected part is saturated with stagnant blood, which promotes the rapid growth of bacteria. The toxic products formed by bacteria are absorbed, causing systemic manifestation of septicemia and finally death.
• Gas gangrene is a bacterial infection that produces gas within tissues. It is a deadly form of gangrene usually caused by Clostridium perfringens bacteria. Infection spreads rapidly as the gases produced by bacteria expand and infiltrate nearby healthy tissue. Because of its ability to quickly spread to surrounding tissues, gas gangrene should be treated as a medical emergency.
• Necrotizing fasciitis affects the deeper layers of the skin.
• Noma is a gangrene of the face.
• Fournier gangrene usually affects the male genitals and groin.
Treatment of gangrene is usually surgical debridement, wound care, and antibiotic therapy, though amputation is necessary in many cases.
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Burkitt’s lymphoma is a very fast growing form of non-Hodgkin’s lymphoma, a cancer in the lymphatic system.
Learning Objectives
• Distinguish between the three variants of Burkitt’s lymphoma: endemic, sporadic and immunodeficiency-associated
Key Points
• Burkitt’s lymphoma was first discovered in children in certain parts of Africa by surgeon Denis Parsons Burkitt, but also occurs in the United States.
• There are three types of Burkitt’s lymphoma: endemic, the sporadic and the immunodeficiency-associated. The endemic type is closely associated with the Epstein-Barr virus (EBV), the main cause of infectious mononucleosis.
• Burkitt’s lymphoma usually develops in the abdomen and spreads to other organs, including the brain. It may first be noticed as a swelling of the lymph nodes (glands) in the neck, groin, or under the arm.
• Chemotherapy and various drugs are used to treat this type of cancer.
Key Terms
• lymph: A colourless, watery, bodily fluid carried by the lymphatic system, that consists mainly of white blood cells.
• lymphoma: A malignant tumor that arises in the lymph nodes or in other lymphoid tissue.
• Non-Hodgkin’s lymphoma: The non-Hodgkin lymphomas are a diverse group of blood cancers that include any kind of lymphoma, except cancers originating from white blood cells called lymphocytes.
Burkitt’s lymphoma is a form of non-Hodgkin’s lymphoma, a cancer of the lymphatic system (in particular, B lymphocytes). It is named after Denis Parsons Burkitt, a surgeon who first described the disease in 1956 while working in equatorial Africa. Burkitt’s lymphoma usually develops in the abdomen and spreads to other organs, including the brain. Burkitt’s lymphoma involves B-cells and is a rapidly growing cancer. Of all cancers involving the same class of blood cell, 2% of cases are Burkitt’s lymphoma.
Classification
Currently Burkitt’s lymphoma can be divided into three main clinical variants:
1. Endemic: This variant occurs in equatorial Africa. It is the most common malignancy affecting children in this area. Children affected with the disease often also have chronic malaria, which is believed to have reduced resistance to Epstein-Barr virus (EBV), allowing it to take hold. The disease characteristically involves the jaw or other facial bone, distal ileum, cecum, ovaries, kidney or the breast.
2. Sporadic: This variant type, also known as “non-African” is found outside of Africa. The tumor cells have a similar appearance to that of endemic Burkitt lymphoma. Again it is believed that impaired immunity provides an opening for development of the Epstein-Barr virus. The jaw is less commonly involved, compared to the endemic variant. The ileo-cecal region is the common site of involvement.
3. Immunodeficiency-associated: Immunodeficiency-associated Burkitt lymphoma is usually associated with HIV infection or occurs in the setting of post-transplant patients who are taking immunosuppressive drugs. Burkitt lymphoma can be one of the diseases associated with the initial manifestation of AIDS.
By morphology (i.e. microscopic appearance) or immunophenotype, it is almost impossible to differentiate these three clinical variants. Immunodeficiency-associated Burkitt lymphoma may demonstrate more plasmacytic appearance or more pleomorphism, but these features are not specific.
Symptoms and Treatment
Burkitt lymphoma may first be noticed as a swelling of the lymph nodes (glands) in the neck, groin, or under the arm. These swollen lymph nodes are often painless, but can grow very rapidly. In the types commonly seen in the United States, the cancer usually starts in the belly area (abdomen). The disease can also start in the ovaries, testes, brain, and spinal fluid. Symptoms include fever, night sweats, unexplained swollen lymph nodes, and unexplained weight loss.
Chemotherapy is used to treat this type of cancer. Commonly used medicines include prednisone, cyclophosphamide, doxorubicin, ifosfamide, vincristine, cytarabine, methotrexate, rituximab, and etoposide. Other treatments are immunotherapy, bone marrow transplants, stem cell transplant, surgery to remove the tumor, and radiotherapy.
15.25B: Infectious Mononucleosis
Learning Objectives
• Describe infectious mononucleosis
Infectious mononucleosis is an infectious, widespread viral disease caused by the Epstein–Barr virus (EBV), one type of herpes virus, to which more than 90% of adults have been exposed. Occasionally, the symptoms can recur at a later period. It is sometimes colloquially known as the “kissing disease” from its oral transmission. Most people are exposed to the virus as children, when the disease produces no noticeable or only flu-like symptoms. In developing countries, people are exposed to the virus in early childhood more often than in developed countries. As a result, the disease in its observable form is more common in developed countries. It is most common among adolescents and young adults.
Symptoms
The disease is characterized by fever, sore throat, and fatigue, along with several other possible signs and symptoms, especially in adolescents and young adults. The infection is spread via saliva and has an incubation period of four to seven weeks. Symptoms usually persist for two to three weeks, but fatigue is often more prolonged. Infectious mononucleosis is primarily diagnosed by observation of symptoms, but suspicion can be confirmed by several diagnostic tests. The most commonly used diagnostic criterion is the presence of 50% lymphocytes with at least 10% atypical lymphocytes (large, irregular nuclei), while the person also has fever, pharyngitis, and adenopathy. Infectious mononucleosis is generally self-limiting, so only symptomatic and/or supportive treatments are used. Rest is recommended during the acute phase of the infection.
Once the acute symptoms of an initial infection disappear, they often do not return. But once infected, the patient carries the virus for the rest of his or her life. The virus typically lives dormantly in B lymphocytes. Independent infections of mononucleosis may be contracted multiple times, regardless of whether the patient is already carrying the virus dormantly.
Key Points
• Infectious mononucleosis is an infectious disease caused by the Epstein-Barr virus (EBV).
• Infectious mononucleosis (also called mono or kissing disease) is spread orally and is characterized by symptoms such as fever, sore throat, and fatigue.
• Once infected, the virus lives dormantly in B lymphocytes in a person.
Key Terms
• Epstein-Barr virus (EBV): Virus responsible for causing infectious mononucelosis.
• infectious mononucleosis: An infectious, widespread viral disease caused by the Epstein–Barr virus (EBV), one type of herpes virus. Most people are exposed to the virus as children, when the disease produces no noticeable or only flu-like symptoms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.25%3A_Viral_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.25A%3A_Burkitts_Lymphoma.txt |
Learning Objectives
• Distinguish between the lytic replicative and latency cycle of the Epstein-Barr virus infection cycle and discuss the prevalence of Epstein-Barr virus infected humans
The Epstein–Barr virus (EBV), also called human herpesvirus 4 (HHV-4), is a virus of the herpes family, and is one of the most common viruses in humans. EBV infection, which occurs by oral transfer of the saliva, results in infectious mononucleosis (glandular fever). It is also associated with particular forms of cancer, such as Hodgkin’s lymphoma, Burkitt’s lymphoma, nasopharyngeal carcinoma, and central nervous system lymphomas associated with HIV. There is evidence that infection with the virus is associated with a higher risk of certain autoimmune diseases, especially dermatomyositis, systemic lupus erythematosus, rheumatoid arthritis, Sjögren’s syndrome, and multiple sclerosis. Most people become infected with EBV and gain adaptive immunity. In the United States, about half of all five-year-old children and 90 to 95 percent of adults have evidence of previous infection. Infants become susceptible to EBV as soon as maternal antibody protection disappears. Many children become infected with EBV, and these infections usually cause no symptoms or are indistinguishable from the other mild, brief illnesses of childhood.
A mature EBV viral particle has a diameter of approximately 120 nm to 180 nm. It is composed of a double stranded, linear DNA genome enclosed by a protein capsid. The capsid is surrounded by a protein tegument, which in turn is surrounded by a lipid envelope. The EBV genome is about 192 thousand base pairs in length and contains about 85 genes. The viral envelope is embedded with glycoproteins essential to viral entry into the cell.
EBV Infection Cycle
EBV infects B cells of the immune system and epithelial cells. Once EBV enters the cell, the viral capsid dissolves and the viral genome is transported to the cell nucleus. An EBV infection can be described as being in one of two cycles; a lytic replicative cycle and a latency cycle.
The lytic cycle, or productive infection, results in the production of infectious virions. EBV can undergo lytic replication in both B cells and epithelial cells. In B cells, lytic replication normally only takes place after reactivation from latency. In epithelial cells, lytic replication often directly follows viral entry entry. For lytic replication to occur, the viral genome must be linear. The latent EBV genome is circular, so it must linearize in the process of lytic reactivation. During lytic replication, viral DNA polymerase is responsible for copying the viral genome. Unlike lytic replication for many other viruses, EBV lytic replication does not inevitably lead to lysis of the host cell because EBV virions are produced by budding from the infected cell.
Unlike lytic replication, the latent stage does not result in production of virions. Instead, the EBV genome circularizes, resides in the cell nucleus as an episome, and is copied by cellular DNA polymerase. In latency, only a portion of EBV’s genes are expressed. Latent EBV expresses its genes in one of three patterns, known as latency programs. EBV can latently persist within B cells and epithelial cells, but different latency programs are possible in the two types of cells. EBV can exhibit one of three latency programs: Latency I, Latency II, or Latency III. Each latency program leads to the production of a limited, distinct set of viral proteins and viral RNAs.
Presence and Symptoms of EBV
The EBV occurs all over the world and most people become infected with this virus at some point in their lives. When teenagers get EBV, there is a 35-50% chance that it will lead to infectious mononucleosis also known as mono. Symptoms of mono include fever, sore throat, pharyngitis, and swollen lymph glands (lymphadenopathy). Although the symptoms of infectious mononucleosis usually go away in 1-2 months, EBV remails dormant and hidden in the troat and blood cells for the rest of the person’s life.
Key Points
• The Epstein–Barr virus (EBV), is a very common virus and infects about 95% of all people in the United States.
• EBV can result in fever, sore throat, pharyngitis, and lymphadenopathy. Together, these symptoms are called infectious mononucleosis.
• An EBV infection can occur in two forms; a lytic replicative stage where it replicates its viral genome and produces gene products to help the virus evade the immune system and a latent stage where it remains undetected until reactivation.
Key Terms
• epithelial cells: cells that are part of the membranous tissue which form the covering of most internal and external surfaces of the body and its organs; internally including the lining of vessels and other small cavities, and externally being the skin.
• lytic cycle: The normal process of viral reproduction involving penetration of the cell membrane, nucleic acid synthesis, and lysis of the host cell.
• B cell: a lymphocyte, developed in the bursa of birds and the bone marrow of other animals, that produces antibodies and is responsible for the immune system. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.25%3A_Viral_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.25C%3A_Other_Diseases_and_Epstein-Barr_Virus.txt |
Cytomegalovirus (CMV) is a type of herpesvirus that largely affects infants and the immunocompromised.
Learning Objectives
• Describe the route of transmission and risks associated with the human cytomegalovirus (HCMV)
Key Points
• Cytomegalovirus (CMV) is a viral genus of the viral family known as Herpesviridae or herpesviruses.
• CMV infections are frequently associated with the salivary glands
• HCMV is found throughout all geographic locations and socioeconomic groups, and infects between 50% and 80% of adults in the United States
• CMV is generally transmitted from infected people to others through direct contact with body fluids, such as urine, saliva, vaginal secretions, and semen.
Key Terms
• immunocompromised: Having an immune system that has been impaired by disease or treatment.
• Seroprevalence: Seroprevalence is the number of persons in a population who test positive for a specific disease based on serology (blood serum) specimens; often presented as a percent of the total specimens tested or as a proportion per 100,000 persons tested.
• major histocompatibility complex: MHC is a cell surface molecule that mediate interactions of immune cells with other leukocytes or body cells. MHC determines compatibility of donors for organ transplants as well as one’s susceptibility to an autoimmune disease. In humans, MHC is also called human leukocyte antigen (HLA).
Cytomegalovirus (CMV) is a viral genus of the viral family known as Herpesviridae or herpesviruses. The species that infects humans is commonly known as human CMV (HCMV) or human herpesvirus-5 (HHV-5), and is the most studied of all cytomegaloviruses. All herpesviruses can stay latent for long durations. Although they may be found throughout the body, CMV infections are frequently associated with the salivary glands in humans and other mammals. Other CMV viruses are found in several mammal species, but species isolated from animals differ from HCMV in terms of genomic structure, and have not been reported to cause human disease.
HCMV is found throughout all geographic locations and socioeconomic groups, and infects between 50% and 80% of adults in the United States (40% worldwide) as indicated by the presence of antibodies in much of the general population. Seroprevalence is age-dependent: 58.9% of individuals aged 6 and older are infected with CMV while 90.8% of individuals aged 80 and older are positive for HCMV. HCMV is also the virus most frequently transmitted to a developing fetus. HCMV infection is more widespread in developing countries and in communities with lower socioeconomic status; it represents the most significant viral cause of birth defects in industrialized countries. Major areas of risk of infection include prenatal or postnatal infants and immunocompromised individuals, such as organ transplant recipients, persons with leukemia, or those infected with human immunodeficiency virus (HIV).
CMV is generally transmitted from infected people to others through direct contact with body fluids, such as urine, saliva, vaginal secretions, and semen. Although they may be found throughout the body, HCMV infections are frequently associated with the salivary glands. HCMV infection is typically unnoticed in healthy people, but can be life-threatening for the immunocompromised, such as HIV-infected persons, organ transplant recipients, or newborn infants.
CMV, like all herpesviruses, can stay latent for long durations of time. The initial introduction of CMV generally gives way to an extended period of infection during which there is no detectable clinical illness. Severe impairment of the body’s immune system reactivates the virus from this dormant state. CMV persists in the host because the viral genome encodes multiple proteins that interfere with major histocompatibility complex (MHC) class I presentation of viral antigens. One viral protein blocks translocation of peptides into the lumen of the endoplasmic reticulum, while two other viral proteins cause degradation of MHC class I proteins before they reach the cell surface. In AIDS patients, CMV can cause loss of vision (cotton wool spots), pneumonia, and hepatitis. Transplant patients with CMV are also susceptible to pneumonia and hepatitis.
A vaccine against (CMV) is currently under investigation. Because CMV can cause congenital infection, considerable effort has been made towards the development of a vaccine, with particular emphasis on protection for pregnant women. There are currently three licensed anti-HCMV drugs target the viral DNA polymerase, pUL54. Ganciclovir (GCV) acts as nucleoside analogue. Its antiviral activity requires phosphorylation by the HCMV protein kinase, pUL97. The second drug, Cidofovir (CDV), is a nucleotide analogue, which is already phosphorylated and thus active. Finally, Foscarnet (FOS) has a different mode of action. It directly inhibits polymerase function by blocking the pyrophosphate binding site of pUL54. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.25%3A_Viral_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.25D%3A_Cytomegalovirus_Infections.txt |
Chikungunya (CHIKV) is a mosquito-borne viral disease which causes fever and severe joint pain.
Learning Objectives
• Discuss the causes and symptoms associated with chikungunya virus (CHIKV)
Key Points
• The chikungunya virus is transmitted from human to human by the bites of infected female mosquitoes; the Aedes aegypti and Aedes albopictus mosquitoes.
• The disease occurs in Africa, Asia and the Indian subcontinent. In recent decades mosquito vectors of CHIKV have spread to Europe and the Americas.
• There is no cure for CHIKV. Treatment is focused on relieving the symptoms which include fever and severe joint pain, muscle pain, headache, nausea, fatigue and rash.
Key Terms
• dengue: An acute febrile disease of the tropics caused by a flavivirus, transmitted by mosquitoes, and characterized by high fever, rash, headache, and severe muscle and joint pain.
• Aedes: Aedes is a genus of mosquito originally found in tropical and subtropical zones, but now found on all continents excluding Antarctica.
• chikungunya: A viral fever caused by an alphavirus spread by mosquito bites.
Chikungunya Virus (CHIKV)
Chikungunya (in the Makonde language “that which bends up”) virus (CHIKV) is an insect-borne virus of the genus Alphavirus, that is transmitted to humans by virus-carrying Aedes(Ae) mosquitoes. Both Ae. aegypti and Ae. albopictus have been implicated in large outbreaks of CHIKV.
CHIKV infection causes an illness with symptoms similar to dengue fever, with an acute febrile phase of the illness lasting only two to five days, followed by a prolonged arthralgic disease that affects the joints of the extremities. The pain associated with CHIKV infection of the joints persists for weeks or months or, in some cases, years. CHIKV is indigenous to tropical Africa and Asia, where it is transmitted to humans by the bite of infected mosquitoes.
SIGNS AND SYMPTOMS
The incubation period of chikungunya disease ranges from one to 12 days, but usually two to three. Its symptoms include a high fever up to 40 °C (104 °F), a petechial or maculopapular rash of the trunk and occasionally the limbs, and arthralgia or arthritis affecting multiple joints. Other nonspecific symptoms can include headache, conjunctivitis, slight photophobia and partial loss of taste. Typically, the fever lasts for two days and then ends abruptly. However, other symptoms—namely joint pain, intense headache, insomnia and an extreme degree of prostration—last for a variable period; usually for about five to seven days. Patients have complained of joint pains for much longer time periods; some for as long as two years, depending on their age.
DIAGNOSIS
Common laboratory tests for chikungunya include RT-PCR, virus isolation, and serological tests.
Virus isolation provides the most definitive diagnosis, but takes one to two weeks for completion and must be carried out in biosafety level-3 laboratories. The technique involves exposing specific cell lines to samples from whole blood and identifying chikungunya virus-specific responses. RT-PCR using nested-primer pairs is used to amplify several chikungunya-specific genes from whole blood. Results can be determined in one to two days. Serological diagnosis requires a larger amount of blood than the other methods, and uses an ELISA assay to measure chikungunya-specific IgM levels. Results require two to three days.
TREATMENT
There are no specific drugs to cure the disease. Treatment is directed primarily at relieving the symptoms, especially the joint pain. There is no commercial chikungunya vaccine.
CHIKUNGUNYA OUTBREAKS
Chikungunya occurs in Africa, Asia, and the Indian subcontinent. Human infections in Africa have been at relatively low levels for a number of years, but in 1999-2000 there was a large outbreak in the Democratic Republic of the Congo, and in 2007 there was an outbreak in Gabon. Starting in February 2005, a major outbreak occurred in islands of the Indian Ocean. A large number of imported cases in Europe were associated with this outbreak, mostly in 2006 when this epidemic was at its peak.
A large outbreak of chikungunya in India occurred in 2006 and 2007. Several other countries in South-East Asia were also affected. In 2007 transmission was reported for the first time in Europe, in a localized outbreak in north-eastern Italy.
15.25F: Classic Viral Hemorrhagic Fevers
Viral hemorrhagic fevers (VHFs) are a group of illnesses that are caused by several distinct families of RNA viruses.
Learning Objectives
• List the types, symptoms and routes of transmission for viral hemorrhagic fevers
Key Points
• VHFs are caused by viruses of four distinct families: arenaviruses, filoviruses, bunyaviruses, and flaviviruses. They are all RNA viruses covered, or enveloped, in a fatty coating.
• Viruses associated with most VHFs naturally reside in an animal host or arthropod vector. For the most part, rodents and arthropods are the main reservoirs for viruses causing VHFs.
• Symptoms include marked fever, fatigue, dizziness, muscle aches, loss of strength, exhaustion, and excessive bleeding under the skin, in internal organs, or from body orifices like the mouth, eyes, or ears.
Key Terms
• hemorrhagic: of, relating to, or producing excessive loss of blood or blood escape from the circulatory system.
The viral hemorrhagic (or haemorrhagic) fevers (VHFs) are a diverse group of animal and human illnesses that may be caused by five distinct families of RNA viruses: the families Arenaviridae, Filoviridae, Bunyaviridae, Flaviviridae, and Rhabdoviridae. All types of VHF are characterized by fever and bleeding disorders and all can progress to high fever, shock and death in many cases. Some of the VHF agents cause relatively mild illnesses, such as the Scandinavian nephropathia epidemica, while others, such as the African Ebola virus, can cause severe, life-threatening disease.
Four families of RNA viruses have been recognized as causing this syndrome:
• The family Arenaviridae include the viruses responsible for Lassa fever, Lujo virus, Argentine, Bolivian, Brazilian and Venezuelan hemorrhagic fevers.
• The family Bunyaviridae include the members of the Hantavirus genus that cause hemorrhagic fever with renal syndrome (HFRS), the Crimean-Congo hemorrhagic fever (CCHF) virus from the Nairovirus genus, Garissa virus from the Orthobunyavirus and the Rift Valley fever (RVF) virus from the Phlebovirus genus.
• The family Filoviridae include Ebola virus and Marburg virus. Ebola has five viral subtypes including Zaire, Sudan, Bundibugyo, Tai Forest (formerly Ivory Coast), and Reston.
• The family Flaviviridae include dengue, yellow fever, and two viruses in the tick-borne encephalitis group that cause VHF: Omsk hemorrhagic fever virus and Kyasanur Forest disease virus.
Transmission
Transmission to humans depends on the specific virus, but includes:
• By contact with the urine, feces, saliva, or blood of animal hosts such as rodents, fruit bats, subhuman primates, and duikers (antelope)
• From mosquito or tick bites
• Contact with vector-infected livestock
• Consuming infected bush meat
Signs and Symptoms
Signs and symptoms of VHFs include fever and bleeding diathesis. Manifestations of VHF often also include flushing of the face and chest, petechiae, frank bleeding, edema, hypotension, and shock. Malaise, myalgias, headache, vomiting, and diarrhea occur frequently. Definitive diagnosis is usually made at a reference laboratory with advanced biocontainment capabilities.
Treatment
For most viral hemorrhagic fevers, there is no effective treatment other than supportive care. The only licensed vaccine available is for yellow fever. Control of rodent populations, insect and other arthropod populations can prevent VHFs. | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.25%3A_Viral_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.25E%3A_Chikungunya_Fever.txt |
As human habitation expands, new viral hemorrhagic fevers are infecting humans.
Learning Objectives
• Generalize the characteristics and implications of an emergent virus
Key Points
• There are several types of viruses that cause hemorrhagic fevers they are typified by high fever and bleeding.
• Emergent viruses are newly discovered viruses, often coming from other animal species. Many emergent viruses are uncovered by human activity such as deforestation.
• New sequencing technologies allow the identification of emergent viruses.
• No other rhabdovirus is known to cause the acute, rapid and deadly hemorrhagic fever seen in the three cases in the Congo.
Key Terms
• Rhabdovirus: Rhabdoviruses are viruses belonging to the family Rhabdoviridae,that infect a broad range of hosts throughout the animal and plant kingdoms.
An emergent virus is a virus that has adapted and emerged as a new disease/pathogenic strain, with attributes facilitating pathogenicity in a field not normally associated with that virus. This includes viruses that are the cause of a disease that has notably increased in incidence; this is often a result of a wide variety of causes from both the influence of man and nature. Most emergent viruses can be categorized as zoonotic; an animal disease that can be transmitted to humans. The virus thus has the advantage of possibly having several natural reservoirs to propagate in. As human development increases, and we move into areas not previously inhabited a reservoir of a virus can be uncovered and infections of humans ensues. This is especially worse in tropical areas of the world with high levels of biodiversity such as Africa, South America, and South Asia. Many newly discovered viruses come from these parts of the world as human habitation expands.
The viral hemorrhagic fevers (VHFs) are a diverse group of animal and human illnesses that may be caused by five distinct families of RNA viruses: the families Arenaviridae, Filoviridae, Bunyaviridae, Flaviviridae, and Rhabdoviridae. All types of VHF are characterized by fever and bleeding disorders and all can progress to high fever, shock and death in many cases. Some of the VHF agents cause relatively mild illnesses, such as the Scandinavian nephropathia epidemica, while others, such as the African Ebola virus, can cause severe, life-threatening disease.
Indeed the advent of deep sequencing technologies and other methods are identifying emergent viral hemorrhagic fevers. A recent study using deep sequencing, discovered a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of three human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a three-week period, were characterized by abrupt disease onset, high fever, bloody vomiting, and diarrhea, and, in two patients, death within three days. BASV was present in the blood of the lone survivor at a concentration of over a million copies per milliliter. The genome of BASV, assembled from over 140 million sequence reads, reveals that it is very different from any other rhabdovirus. The lone survivor and a nurse caring for him (with no symptoms), both health care workers, were found to have high levels of antibodies to BASV, indicating that they both had been infected by the virus. Although the source of the virus remains unclear, the study findings suggest that BASV may be spread by human-to-human contact and is an emerging pathogen associated with acute hemorrhagic fever in Africa.
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• PLOS Pathogens: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa. Provided by: PLOS Pathogens. Located at: www.plospathogens.org/article...t.1002924.g001. License: CC BY: Attribution | textbooks/bio/Microbiology/Microbiology_(Boundless)/15%3A_Diseases/15.25%3A_Viral_Diseases_of_the_Cardiovascular_and_Lymphatic_Systems/15.25G%3A_Emerging_Viral_Hemorrhagic_Fevers.txt |
Thumbnail: Hydrothermal vents are cracks in the earth’s crust where geothermally heated water leaks out.
16: Microbial Ecology
Every ecosystem on Earth contains microorganisms that occupy unique niches based on their specific metabolic properties.
Learning Objectives
• Evaluate microbes and the niches they occupy
Key Points
• Microbes live in all parts of the biosphere where there is liquid water.
• By virtue of their omnipresence, microbes impact the entire biosphere.
• Each microbial species in an ecosystem is thought to occupy a unique niche, which is a complex description of the ways in which an organism uses its environment.
• The precise ecological niche of a microbe is primarily determined by the specific metabolic properties of that organism.
Key Terms
• bioremediation: The use of biological organisms, usually microorganisms, to remove contaminants, especially from polluted water.
• niche: A function within an ecological system to which an organism is especially suited.
• biosphere: The part of the Earth and its atmosphere capable of supporting life.
Microbes and Ecosystem Niches
Microbial life is amazingly diverse and microorganisms quite literally cover the planet. In fact, it has been estimated that there are 100,000,000 times more microbial cells on the planet than there are stars in the observable universe! Microbes live in all parts of the biosphere where there is liquid water, including soil, hot springs, the ocean floor, acid lakes, deserts, geysers, rocks, and even the mammalian gut.
By virtue of their omnipresence, microbes impact the entire biosphere; indeed, microbial metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) collectively control global biogeochemical cycling. The ability of microbes to contribute substantially to the function of every ecosystem is a reflection their tremendous biological diversity.
Microbes are vital to every ecosystem on Earth and are particularly important in zones where light cannot approach (that is, where photosynthesis cannot be the basic means to collect energy). Microorganisms participate in a host of fundamental ecological processes including production, decomposition, and fixation. They can also have additional indirect effects on the ecosystem through symbiotic relationships with other organisms. In addition, microbial processes can be co-opted for biodegradation or bioremediation of domestic, agricultural, and industrial wastes, making the study of microbial ecology particularly important for biotechnological and environmental applications.
Each species in an ecosystem is thought to occupy a separate, unique niche. The ecological niche of a microorganism describes how it responds to the distribution of resources and competing species, as well as the ways in which it alters those same factors in turn. In essence, the niche is a complex description of the ways in which a microbial species uses its environment.
The precise ecological niche of a microbe is primarily determined by the specific metabolic properties of that organism. For example, microbial organisms that can obtain energy from the oxidation of inorganic compounds (such as iron-reducing bacteria ) will likely occupy a different niche from those that obtain energy from light (such as cyanobacteria). Even among photosynthetic bacteria, there are various species that contain different photosynthetic pigments (such as chlorophylls and carotenoids) that allow them to take advantage of different portions of the electromagnetic spectrum; therefore, even microbes with similar metabolic properties may inhabit unique niches. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.01%3A_Microbial_Ecology/16.1A%3A_Microbes_and_Ecosystem_Niches.txt |
Microorganisms serve essential roles in the complex nutrient exchange system that defines an ecological community.
Learning Objectives
• Illustrate the organization of ecosystems
Key Points
• An ecosystem is a unified system of exchange made up of autotrophic producers, heterotrophic consumers, and decomposers.
• A food web depicts a collection of heterotrophic consumers that network and cycle the flow of energy and nutrients from a productive base of self-feeding autotrophs.
• Microorganisms play a vital role in every ecological community by serving as both producers and decomposers.
Key Terms
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
• heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.
Although ecologists tend to regard ecosystems as basic structural units, it can be difficult (if not impossible) to formally define the boundaries of a given ecosystem. As such, ecosystems are better thought of as conceptual rather than actual geographical locations. Rarely are ecosystems isolated from one another; rather, they should be considered parts of a larger functioning whole that together comprise the biosphere (“the place on Earth’s surface where life dwells”).
Despite the fact that clear boundaries between ecosystems may be difficult to identify, the myriad interactions that take place within an ecological community can often be observed and defined. These interactions may be best described by detailing feeding connections (what eats what) among biota in an ecosystem, thereby linking the ecosystem into a unified system of exchange.
All life forms in an ecosystem can be broadly grouped into one of two categories (called trophic levels):
• Autotrophs, which produce organic matter (food) from inorganic substances; and
• Heterotrophs, which must feed on other organisms in order to obtain organic matter.
In general, trophic levels are used to describe the way in which a particular organism within an ecosystem gets its food. Using this description, we can restate and reorganize the categories above to define the three basic ways organisms acquire their food:
• Producers (autotrophs) do not usually eat other organisms but pull nutrients from the soil or the ocean and manufacture their own food using photosynthesis. In this way, it is the energy from the sun that usually powers the base of the food chain.
• Consumers (heterotrophs) cannot manufacture their own food and need to consume other organisms.
• Decomposers break down dead plant and animal material and wastes and release them into the ecosystem as energy and nutrients for recycling.
Within ecosystems, the biotic factors that comprise the categories above can be organized into a food chain in which autotrophic producers use materials and nutrients recycled by decomposers to make their own food; the producers are in turn eaten by heterotrophic consumers. In real world ecosystems, there are multiple food chains for most organisms (since most organisms eat more than one kind of food or are eaten by more than one type of predator). Additionally, the movement of mineral nutrients in the food chain is cyclic rather than linear. As a consequence, the intricate network of intersecting and overlapping food chains for an ecosystem is more commonly represented as a food web. A food web depicts a collection of heterotrophic consumers that network and cycle the flow of energy and nutrients from a productive base of self-feeding autotrophs.
Microorganisms play a vital role in every ecological community by serving both as producers and as decomposers. Although plants are the most common primary producers, autotrophic photosynthetic microbes (such as cyanobacteria and algae) can harness light energy to generate organic matter. Additionally, in zones where light cannot penetrate (and thus photosynthesis cannot be the basic means to produce energy), chemosynthetic microbes provide energy and carbon to the other organisms in the ecosystem. Other microbes are decomposers, with the ability to recycle nutrients from dead organic matter and other organisms’ waste products. Decomposition is critical as most of the carbon and energy incorporated into plant tissues during photosynthesis remains uneaten when the plant tissue dies (and therefore must be broken down before it can be made available for recycling). | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.01%3A_Microbial_Ecology/16.1B%3A_Organization_of_Ecosystems.txt |
Microbes form the backbone of every ecological system by controlling global biogeochemical cycling of elements essential for life.
Learning Objectives
• Explain the role microbes play in biogeochemical cycling
Key Points
• A biogeochemical cycle is a pathway by which a chemical element (such as carbon or nitrogen) circulates through and is recycled by an ecosystem.
• Microorganisms play a primary role in regulating biogeochemical systems in virtually all of our planet ‘s environments.
• Microbes participate in essential biogeochemical cycling events such as carbon and nitrogen fixation.
Key Terms
• photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
• biogeochemistry: The scientific study of biological, geological, and chemical processes in the natural environment and especially of their mutual relationships.
• nitrogenase: The enzyme, in nitrogen-fixing bacteria, that catalyzes the conversion of atmospheric nitrogen into ammonia.
Microbial Role in Biogeochemical Cycling
Nutrients move through the ecosystem in biogeochemical cycles. A biogeochemical cycle is a pathway by which a chemical element (such as carbon or nitrogen) circulates through the biotic (living) and the abiotic (non-living) factors of an ecosystem. The elements that move through the factors of an ecosystem are not lost but are instead recycled or accumulated in places called reservoirs (or “sinks”) where they can be held for a long period of time. Elements, chemical compounds, and other forms of matter are passed from one organism to another and from one part of the biosphere to another through these biogeochemical cycles.
Ecosystems have many biogeochemical cycles operating as a part of the system. A good example of a molecule that is cycled within an ecosystem is water, which is always recycled through the water cycle. Water undergoes evaporation, condensation, and then falls back to Earth as rain (or other forms of precipitation). This typifies the cycling that is observed for all of the principal elements of life.
Although biogeochemical cycles in a given ecosystem are coordinated by the full complement of living organisms and abiotic factors that make up that system, microorganisms play a primary role in regulating biogeochemical systems in virtually all of our planet’s environments. This includes extreme environments such as acid lakes and hydrothermal vents, and even includes living systems such as the human gut. The key collective metabolic processes of microbes (including nitrogen fixation, carbon fixation, methane metabolism, and sulfur metabolism) effectively control global biogeochemical cycling. Incredibly, production by microbes is so immense that global biogeochemistry would likely not change even if eukaryotic life were totally absent!
Microbes comprise the backbone of every ecological system, particularly those in which there is no light (i.e. systems in which energy cannot be collected through photosynthesis ). Two key examples of critical biogeochemical processes carried out by microorganisms are discussed below.
The Carbon Cycle
Carbon is critical for life because it is the essential building block of all organic compounds. Plants and animals utilize carbon to produce carbohydrates, fats, and proteins, which can then be used to build their internal structures or to obtain energy.
Carbon in the form of carbon dioxide (CO2) is readily obtained from the atmosphere, but before it can be incorporated into living organisms it must be transformed into a usable organic form. The transformative process by which carbon dioxide is taken up from the atmospheric reservoir and “fixed” into organic substances is called carbon fixation. Perhaps the best known example of carbon fixation is photosynthesis, a process by which energy derived from sunlight is harnessed to form organic compounds. Photosynthesis depends on the activity of microorganisms such as cyanobacteria; indeed, the fact that there is oxygen in the Earth’s atmosphere at all is a consequence of the photosynthetic activity of ancient microbes.
The Nitrogen Cycle
Nitrogen is essential for all forms of life because it is required for synthesis of the basic building blocks of life (e.g., DNA, RNA, and amino acids). The Earth’s atmosphere is primarily composed of nitrogen, but atmospheric nitrogen (N2) is relatively unusable for biological organisms. Consequently, chemical processing of nitrogen (or nitrogen fixation) is necessary to convert gaseous nitrogen into forms that living organisms can use. Almost all of the nitrogen fixation that occurs on the planet is carried out by bacteria that have the enzyme nitrogenase, which combines N2 with hydrogen to produce a useful form of nitrogen (such as ammonia). Thus, microorganisms are absolutely essential for plant and animal life forms, which cannot fix nitrogen on their own. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.01%3A_Microbial_Ecology/16.1C%3A_Role_of_Microbes_in_Biogeochemical_Cycling.txt |
The extraordinary biological diversity among microbes reflects their ability to occupy every habitable environment on the planet.
Learning Objectives
• Define microenvironments
Key Points
• Microorganisms are found in practically every habitat present on the planet.
• Microorganisms have evolved to survive in extraordinarily diverse environments, including extreme, hostile, or otherwise intolerant ecological systems.
• In addition to occupying a unique niche within an ecosystem, microbes adapt to microenvironments (or microhabitats) that can be distinguished from the immediate surroundings by such factors as the amount of incident light, the degree of moisture, and the range of temperatures.
Key Terms
• microenvironment: The very small environment in the immediate vicinity of an organism.
• extremophilic: Of or pertaining to the extremophiles, a class of organism that thrives under extreme conditions of temperature, salinity, and so on; commercially important as a source of enzymes that operate under similar conditions.
• ubiquitous: Being everywhere at once: omnipresent.
Microorganisms are found on practically every habitable square inch of the planet. They live and thrive in all parts of the biosphere where there is liquid water, including hostile environments such as the poles, deserts, geysers, rocks, and the deep sea. Additionally, while microbes are often free-living, many have intimate symbiotic relationships with other larger organisms. Clearly, microbes have adapted to extreme and intolerant conditions, and it is this adaptation that has yielded tremendous biological diversity among microorganisms.
Like all extant organisms, microbes have evolved to thrive within a given environmental context. Microorganisms are ubiquitous despite the fact that the planet is host to extraordinarily diverse environments. Therefore, microbes have adapted to fill every ecological niche on the planet. For example, extremophilic species have been found that can tolerate the following environmental extremes:
• Temperatures as high as 130 °C (266 °F) and as low as −17 °C (1 °F)
• Highly alkaline (pH 0) and highly acidic (pH 11.5) environments
• Extremely saline environments (including those in which the salt concentration is saturating)
• Extremely high (1,000-2,000 atm) and low (0 atm) pressures (some bacteria can survive for prolonged periods in a pressure-less vacuum, meaning they might even survive in space)
• High ionizing radiation (up to 15,000 Gy; as a reference, a mere 5 Gy would kill a human! )
These evolutionary adaptations have allowed microbial life to extend into much of the Earth’s atmosphere, crust, and hydrosphere (the water found over, under, and on the surface of a planet).
In addition to occupying a unique niche within an ecosystem, microbes are potentially sensitive to subtle environmental differences between adjacent areas. These differences define so-called microenvironments (or microhabitats) that can be distinguished from the immediate surroundings by such factors as the amount of incident light, the degree of moisture, and the range of temperatures. For example, the side of a tree that is shaded from sunlight is a microenvironment that typically supports a somewhat different community of microorganisms than would be found on the side that receives regular light. Microbes, therefore, are not only adapted to their habitat, but also to the immediate environment, thus promoting increased diversity among microbial species within an ecosystem.
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Learning Objectives
• Explain soil composition
Plants obtain inorganic elements from the soil, which serves as a natural medium for land plants. Soil is the outer, loose layer that covers the surface of Earth. Soil quality, a major determinant, along with climate, of plant distribution and growth, depends not only on the chemical composition of the soil, but also the topography (regional surface features) and the presence of living organisms.
Soil consists of these major components:
• inorganic mineral matter, about 40 to 45 percent of the soil volume
• organic matter, about 5 percent of the soil volume
• water, about 25 percent of the soil volume
• air, about 25 percent of the soil volume
The amount of each of the four major components of soil depends on the quantity of vegetation, soil compaction, and water present in the soil. A good, healthy soil has sufficient air, water, minerals, and organic material to promote and sustain plant life.
The organic material of soil, called humus, is made up of microorganisms (dead and alive), and dead animals and plants in varying stages of decay. Humus improves soil structure, providing plants with water and minerals. The inorganic material of soil is composed of rock, slowly broken down into smaller particles that vary in size. Soil particles that are 0.1 to 2 mm in diameter are sand. Soil particles between 0.002 and 0.1 mm are called silt, and even smaller particles, less than 0.002 mm in diameter, are called clay. Some soils have no dominant particle size, containing a mixture of sand, silt, and humus; these soils are called loams.
Key Points
• The chemical composition of the soil, the topography, and the presence of living organisms determines the quality of soil.
• In general, soil contains 40-45% inorganic matter, 5% organic matter, 25% water, and 25% air.
• In order to sustain plant life, the proper mix of air, water, minerals, and organic material is required.
• Humus, the organic material in soil, is composed of microorganisms (dead and alive) and decaying plants.
• The inorganic material of soil is composed of rock, which is broken down into small particles of sand (0.1 to 2 mm), silt (0.002 to 0.1 mm), and clay (less than 0.002 mm).
• Loam is a soil that is a mix sand, silt, and humus.
Key Terms
• loam: soil with no dominant particle size that contains a mixture of sand, silt, and humus
• humus: a large group of natural organic compounds found in the soil composed of decaying plants and dead and living microorganisms
16.2B: Physical Properties of Soil
Learning Objectives
• Describe the physical properties or profile of soil
Soils are named and classified based on their horizons. The soil profile has four distinct layers:
1. The O horizon has freshly-decomposing organic matter, humus, at its surface, with decomposed vegetation at its base. Humus enriches the soil with nutrients, enhancing soil moisture retention. Topsoil, the top layer of soil, is usually two to three inches deep, but this depth can vary considerably. For instance, river deltas, such as the Mississippi River delta, have deep layers of topsoil. Topsoil is rich in organic material. Microbial processes occur there; it is responsible for plant production.
2. The A horizon consists of a mixture of organic material with inorganic products of weathering; it is the beginning of true mineral soil. This horizon is typically darkly colored because of the presence of organic matter. In this area, rainwater percolates through the soil and carries materials from the surface.
3. The B horizon, or subsoil, is an accumulation of mostly fine material that has moved downward, resulting in a dense layer in the soil. In some soils, the B horizon contains nodules or a layer of calcium carbonate.
4. The C horizon, or soil base, includes the parent material, plus the organic and inorganic material that is broken down to form soil. The parent material may be either created in its natural place or transported from elsewhere to its present location. Beneath the C horizon lies bedrock.
Some soils may have additional layers, or lack one of these layers. The thickness of the layers is also variable, depending on the factors that influence soil formation. In general, immature soils may have O, A, and C horizons, whereas mature soils may display all of these, plus additional layers.
Key Points
• The O horizon, or topsoil, is made of decaying organisms and plant life; it is responsible for plant production.
• The A horizon is of a mixture of organic material and inorganic products of weathering; it is the beginning of true mineral soil.
• The B horizon, or subsoil, is a dense layer of mostly fine material that has been pushed down from the topsoil.
• The C horizon, or soil base, is located just above bedrock and is made of parent, organic, and inorganic material.
Key Terms
• topsoil: top layer of soil containing humus at its surface and decomposing vegetation at its base; the most fertile soil
• subsoil: dense layer of soil containing fine material that has moved downward; the layer of earth that is below the topsoil | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2A%3A_Soil_Composition.txt |
A mycorrhiza is a symbiotic association between a fungus and the roots of a vascular plant.
Learning Objectives
• Evaluate mycorrhiza as a plant symbiote
Key Points
• In a mycorrhizal association, the fungus colonizes the host plant’s roots, either intracellularly as in arbuscular mycorrhizal fungi (AMF or AM) or extracellularly as in ectomycorrhizal fungi.
• Mycorrhiza are named after their presence in the plant’s rhizosphere (root system). This mutualistic association provides the fungus with relatively constant and direct access to carbohydrates, such as glucose and sucrose.
• Plants grown in sterile soils and growth media often perform poorly without the addition of spores or hyphae of mycorrhizal fungi to colonize the plant roots and aid in the uptake of soil mineral nutrients.
Key Terms
• mycorrhiza: A symbiotic relationship between the mycelium of a fungus and the roots of a plant.
A mycorrhiza is a symbiotic (generally mutualistic, but occasionally weakly pathogenic) association between a fungus and the roots of a vascular plant.
In a mycorrhizal association, the fungus colonizes the host plant’s roots, either intracellularly as in arbuscular mycorrhizal fungi (AMF or AM) or extracellularly as in ectomycorrhizal fungi. They are an important component of soil life and soil chemistry. Mycorrhizas form a mutualistic relationship with the roots of most plant species. While only a small proportion of all species has been examined, 95% of those plant families are predominantly mycorrhizal.
They are named after their presence in the plant’s rhizosphere (root system). This mutualistic association provides the fungus with relatively constant and direct access to carbohydrates, such as glucose and sucrose. The carbohydrates are translocated from their source (usually leaves) to root tissue and on to the plant’s fungal partners. In return, the plant gains the benefits of the mycelium’s higher absorptive capacity for water and mineral nutrients due to the comparatively large surface area of mycelium: root ratio, thus improving the plant’s mineral absorption capabilities. Plant roots alone may be incapable of taking up phosphate ions that are demineralized in soils with a basic pH. The mycelium of the mycorrhizal fungus can, however, access these phosphorus sources and make them available to the plants they colonize.
Suillus tomentosus, a fungus, produces specialized structures, known as tuberculate ectomycorrhizae, with its plant host lodgepole pine (Pinus contorta var. latifolia). These structures have in turn been shown to host nitrogen fixing bacteria which contribute a significant amount of nitrogen and allow the pines to colonize nutrient-poor sites.
Plants grown in sterile soils and growth media often perform poorly without the addition of spores or hyphae of mycorrhizal fungi to colonize the plant roots and aid in the uptake of soil mineral nutrients.
Fungi have been found to have a protective role for plants rooted in soils with high metal concentrations, such as acidic and contaminated soils. Pine trees inoculated with Pisolithus tinctorius planted in several contaminated sites displayed high tolerance to the prevailing contaminant, survivorship, and growth.
Mycorrhizas are present in 92% of plant families studied (80% of species), with arbuscular mycorrhizas being the ancestral and predominant form and the most prevalent symbiotic association found in the plant kingdom. The structure of arbuscular mycorrhizas has been highly conserved since their first appearance in the fossil record. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2C%3A_Mycorrhiza.txt |
Wetlands are considered one of the most biologically diverse of all ecosystems.
Learning Objectives
• Assess the composition of wetland soils
Key Points
• Nutrient cycling in lakes and freshwater wetlands depends heavily on redox conditions.
• Some anaerobic microbial processes include denitrification, sulfate reduction and methanogenesis and are responsible for the release of N2 (nitrogen), H2S (hydrogen sulfide) and CH4 (methane).
• Other anaerobic microbial processes are linked to changes in the oxidation state of iron and manganese and as a result of anaerobic decomposition, the soil stores large amounts of organic carbon because decomposition is incomplete.
Key Terms
• denitrification: The process by which a nitrate becomes molecular nitrogen, especially by the action of bacteria.
• methanogenesis: The generation of methane by anaerobic bacteria.
• heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.
A wetland is a land area that is saturated with water, either permanently or seasonally, such that it takes on the characteristics of a distinct ecosystem. Primarily, the factor that distinguishes wetlands from other land forms or water bodies is the characteristic vegetation that is adapted to its unique soil conditions: Wetlands consist primarily of hydric soil, which supports aquatic plants. The water found in wetlands can be saltwater, freshwater, or brackish. Main wetland types include swamps, marshes, bogs and fens. Sub-types include mangrove, carr, pocosin, and varzea.
Wetlands play a number of roles in the environment, principally water purification, flood control, and shoreline stability. Wetlands are also considered the most biologically diverse of all ecosystems, serving as home to a wide range of plant and animal life.
In balanced soil, plants grow in an active and steady environment. The mineral content of the soil and its heartiful structure are important for their well-being, but it is the life in the earth that powers its cycles and provides its fertility. Without the activities of soil organisms, organic materials would accumulate and litter the soil surface, and there would be no food for plants.
The soil biota includes:
Megafauna: size range – 20 mm upward, e.g. moles, rabbits, and rodents.
Mesofauna: size range – 100 micrometres to 2 mm, e.g. tardigrades, mites, and springtails.
Microfauna and Microflora: size range – 1 to 100 micrometres, e.g. yeasts, bacteria (commonly actinobacteria), fungi, protozoa, roundworms, and rotifers.
Of these, bacteria and fungi play key roles in maintaining a healthy soil. They act as decomposers that break down organic materials to produce detritus and other breakdown products. Soil detritivores, like earthworms, ingest detritus and decompose it. Saprotrophs, well represented by fungi and bacteria, extract soluble nutrients from delitro. The ants (macrofaunas) help by breaking down in the same way but they also provide the motion part as they move in their armies. Also the rodents, wood-eaters help the soil to be more absorbent.
Nutrient cycling in lakes and freshwater wetlands depends heavily on redox conditions. Under a few millimeters of water heterotrophic bacteria metabolize and consume oxygen. They therefore deplete the soil of oxygen and create the need for anaerobic respiration. Some anaerobic microbial processes include denitrification, sulfate reduction and methanogenesis and are responsible for the release of N2 (nitrogen), H2S (hydrogen sulfide) and CH4 (methane). Other anaerobic microbial processes are linked to changes in the oxidation state of iron and manganese. As a result of anaerobic decomposition, the soil stores large amounts of organic carbon because decomposition is incomplete.
The redox potential describes which way chemical reactions will proceed in oxygen deficient soils and controls the nutrient cycling in flooded systems. Redox potential, or reduction potential, is used to express the likelihood of an environment to receive electrons and therefore become reduced. For example, if a system already has plenty of electrons (anoxic, organic-rich shale) it is reduced and will likely donate electrons to a part of the system that has a low concentration of electrons, or an oxidized environment, to equilibrate to the chemical gradient. The oxidized environment has high redox potential, whereas the reduced environment has a low redox potential.
The redox potential is controlled by the oxidation state of the chemical species, pH and the amount of oxygen (O2) there is in the system. The oxidizing environment accepts electrons because of the presence of O2, which acts as electron acceptors:
O2 + 4e + 4H+ → H2O
This equation will tend to move to the right in acidic conditions which causes higher redox potentials to be found at lower pH levels. Bacteria, heterotrophic organisms, consume oxygen while decomposing organic material which depletes the soils of oxygen, thus increasing the redox potential. In low redox conditions the deposition of ferrous iron (Fe2+) will increase with decreasing decomposition rates, thus preserving organic remains and depositing humus. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2D%3A_Wetland_Soils.txt |
An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life without causing apparent disease.
Learning Objectives
• Evaluate endophytes as plant pathogens
Key Points
• Endophytes are ubiquitous and have been found in all the species of plants studied to date.
• Vertically transmitted fungal endophytes are asexual and transmit via fungal hyphae penetrating the host ‘s seeds (e.g., Neotyphodium).
• The wide range of compounds produced by endophytes have been shown to combat pathogens and even cancers in animals including humans.
Key Terms
• endophyte: Any organism that lives inside another plant.
An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life without causing apparent disease. Endophytes are ubiquitous and have been found in all the species of plants studied to date. However, most of these endophyte/plant relationships are not well understood. Many economically important forage and turfgrasses (e.g., Festuca spp., Lolium spp.) carry fungal endophytes (Neotyphodium spp.) which may improve the ability of these grasses to tolerate abiotic stresses such as drought, as well as improve their resistance to insect and mammalian herbivores.
Endophytes may be transmitted either vertically (directly from parent to offspring) or horizontally (from individual to unrelated individual). Vertically transmitted fungal endophytes are asexual and transmit via fungal hyphae penetrating the host’s seeds (e.g., Neotyphodium). Since their reproductive fitness is intimately tied to that of their host plant, these fungi are often mutualistic. Conversely, horizontally transmitted fungal endophytes are sexual and transmit via spores that can be spread by wind and/or insect vectors. Since they spread in a similar way to pathogens, horizontally transmitted endophytes are often closely related to pathogenic fungi, although they are not pathogenic themselves.
Endophytes may benefit host plants by preventing pathogenic organisms from colonizing them. Extensive colonization of the plant tissue by endophytes creates a “barrier effect,” where the local endophytes outcompete and prevent pathogenic organisms from taking hold. Endophytes may also produce chemicals which inhibit the growth of competitors, including pathogenic organisms. Some bacterial endophytes have proven to increase plant growth. The presence of fungal endophytes can cause higher rates of water loss in leaves. However, certain fungal endophytes help plants survive drought and heat. Plant use of endophytic fungi in defense is a very common phenomenon, primarily involving the arbuscular mycorrhizal fungi.
The wide range of compounds produced by endophytes have been shown to combat pathogens and even cancers in animals including humans. One notable endophyte with medicinal benefits to humans was discovered by Gary Strobel: Pestalotiopsis microspora, an endophytic fungus of Taxus wallachiana (Himalayan Yew) was found to produce taxol. Endophytes are also being investigated for roles in agriculture and biofuels production. Inoculating crop plants with certain endophytes may provide increased disease or parasite resistance while others may possess metabolic processes that convert cellulose and other carbon sources into “myco-diesel” hydrocarbons and hydrocarbon derivatives. Piriformospora indica is an interesting endophytic fungus of the order Sebacinales, the fungus is capable of colonizing roots and forming symbiotic relationship with every possible plant on earth. P. indica has also been shown to increase both crop yield and plant defence of a variety of crops (barley, tomato, maize, etc. ) against root-pathogens.
It is speculated that there may be many thousands of endophytes useful to mankind. However, since there are few scientists working in this field, and since forests and areas of biodiversity are rapidly being destroyed, many useful endophytes for curing disease might be permanently lost for medicinal use before they are discovered. The effects of climate change on endophytes are being investigated. Studies of plants grown at different climates or at increased carbon dioxide levels have different distributions of endophytic species. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2E%3A_Endophytes_and_Plants.txt |
Many plants form associations called mycorrhizae with fungi that give them access to nutrients in the soil, protecting against disease and toxicities.
Learning Objectives
• Describe the symbiotic relationship of mycorrhizae and plant roots
Key Points
• Because nutrients are often depleted in the soil, most plants form symbiotic relationships called mycorrhizae with fungi that integrate into the plant’s root.
• The relationship between plants and fungi is symbiotic because the plant obtains phosphate and other minerals through the fungus, while the fungus obtains sugars from the plant root.
• The long extensions of the fungus, called hyphae, help increase the surface area of the plant root system so that it can extend beyond the area of nutrient depletion.
• Ectomycorrhizae are a type of mycorrhizae that form a dense sheath around the plant roots, called a mantle, from which the hyphae grow; in endomycorrhizae, mycelium is embedded within the root tissue, as opposed to forming a sheath around it.
• In endomycorrhizae, mycelium is embedded within the root tissue, as opposed to forming a sheath around it; these are found in the roots of most terrestrial plants.
Key Terms
• mycorrhiza: a symbiotic association between a fungus and the roots of a vascular plant
• hypha: a long, branching, filamentous structure of a fungus that is the main mode of vegetative growth
• mycelium: the vegetative part of any fungus, consisting of a mass of branching, threadlike hyphae, often underground
Mycorrhizae: The Symbiotic Relationship between Fungi and Roots
Mycorrhizae: Hyphae proliferate within the mycorrhizae, which appears as off-white fuzz in this image. These hyphae greatly increase the surface area of the plant root, allowing it to reach areas that are not depleted of nutrients.
A nutrient depletion zone can develop when there is rapid soil solution uptake, low nutrient concentration, low diffusion rate, or low soil moisture. These conditions are very common; therefore, most plants rely on fungi to facilitate the uptake of minerals from the soil. Mycorrhizae, known as root fungi, form symbiotic associations with plant roots. In these associations, the fungi are actually integrated into the physical structure of the root. The fungi colonize the living root tissue during active plant growth.
Through mycorrhization, the plant obtains phosphate and other minerals, such as zinc and copper, from the soil. The fungus obtains nutrients, such as sugars, from the plant root. Mycorrhizae help increase the surface area of the plant root system because hyphae, which are narrow, can spread beyond the nutrient depletion zone. Hyphae are long extensions of the fungus, which can grow into small soil pores that allow access to phosphorus otherwise unavailable to the plant. The beneficial effect on the plant is best observed in poor soils. The benefit to fungi is that they can obtain up to 20 percent of the total carbon accessed by plants. Mycorrhizae function as a physical barrier to pathogens. They also provides an induction of generalized host defense mechanisms, which sometimes involves the production of antibiotic compounds by the fungi. Fungi have also been found to have a protective role for plants rooted in soils with high metal concentrations, such as acidic and contaminated soils.
There are two types of mycorrhizae: ectomycorrhizae and endomycorrhizae. Ectomycorrhizae form an extensive dense sheath around the roots, called a mantle. Hyphae from the fungi extend from the mantle into the soil, which increases the surface area for water and mineral absorption. This type of mycorrhizae is found in forest trees, especially conifers, birches, and oaks. Endomycorrhizae, also called arbuscular mycorrhizae, do not form a dense sheath over the root. Instead, the fungal mycelium is embedded within the root tissue. Endomycorrhizae are found in the roots of more than 80 percent of terrestrial plants. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2F%3A_Mycorrhizae-_The_Symbiotic_Relationship_between_Fungi_and_Roots.txt |
There are four main bacterial pathogenicity factors: cell wall degrading enzymes, toxins, phytohormones, and effector proteins.
Learning Objectives
• Break down the types and modes of plant pathogenicity
Key Points
• The majority of phytopathogenic fungi belong to the Ascomycetes and the Basidiomycetes.
• Many soil inhabiting fungi are capable of living saprotrophically, carrying out the part of their lifecycle in the soil.
• Bacterial plant pathogens are much more prevalent in sub-tropical and tropical regions of the world.
Key Terms
• Type three secretion system: Type three secretion system (often written Type III secretion system and abbreviated TTSS or T3SS, also called Injectisome or Injectosome) is a protein appendage found in several Gram-negative bacteria. In pathogenic bacteria, the needle-like structure is used as a sensory probe to detect the presence of eukaryotic organisms and secrete proteins that help the bacteria infect them. The proteins are secreted directly from the bacterial cell into the eukaryotic cell, also known as “the host” cell.
Most bacteria that are associated with plants are actually saprophytic, and do no harm to the plant itself. However, a small number, around 100 species, are able to cause disease. Bacterial diseases are much more prevalent in sub-tropical and tropical regions of the world. Most plant pathogenic bacteria are rod shaped (bacilli). In order to be able to colonise the plant they have specific pathogenicity factors. There are 4 main bacterial pathogenicity factors:
• Cell wall -degrading enzymes: These are used to break down the plant cell wall in order to release the nutrients inside.
• Toxins: These can be non- host -specific, which damage all plants, or host-specific, which cause damage only on a host plant.
• Phytohormones: example Agrobacterium changes the level of Auxin to cause tumours.
• Effector proteins: These can be secreted into the extracellular environment or directly into the host cell, often via the Type three secretion system. Some effectors are known to suppress host defense processes. This can include: reducing the plants internal signaling mechanisms or reduction of phytochemicals production. Bacteria, fungus and oomycetes are known for this function.
Significant bacterial plant pathogens:
• Burkholderia
• Proteobacteria
• Xanthomonas spp.
• Pseudomonas spp.
• Pseudomonas syringae pv. tomato causes tomato plants to produce less fruit, and it “continues to adapt to the tomato by minimizing its recognition by the tomato immune system. “
The majority of phytopathogenic fungi belong to the Ascomycetes and the Basidiomycetes. The fungi reproduce both sexually and asexually via the production of spores and other structures. Spores may be spread long distances by air or water, or they may be soil borne. Many soil inhabiting fungi are capable of living saprotrophically, carrying out the part of their lifecycle in the soil. These are known as facultative saprotrophs. Fungal diseases may be controlled through the use of fungicides and other agriculture practices, however new races of fungi often evolve that are resistant to various fungicides. · Biotrophic fungal pathogens colonize living plant tissue and obtain nutrients from living host cells. Necrotrophic fungal pathogens infect and kill host tissue and extract nutrients from the dead host cells.
Significant fungal plant pathogens include:
• Fusarium spp. (causal agents of Fusarium wilt disease)
• Thielaviopsis spp. (causal agents of: canker rot, black root rot, Thielaviopsis root rot)
• Verticillium spp.
• Magnaporthe grisea (causal agent of blast of rice and gray leaf spot in turfgrasse
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• OpenStax College, The Soil. October 17, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44715/latest...e_31_02_01.png. License: CC BY: Attribution
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• OpenStax College, Nutritional Adaptations of Plants. October 17, 2013. Provided by: OpenStax CNX. Located at: http://cnx.org/content/m44718/latest...31_03_02ab.jpg. License: CC BY: Attribution | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2F%3A_Plant_Pathogens.txt |
Plants cannot extract the necessary nitrogen from soil, so they form symbiotic relationships with rhizobia that can fix it as ammonia.
Learning Objectives
• Explain the process and importance of nitrogen fixation
Key Points
• Diatomic nitrogen is abundant in the atmosphere and soil, but plants are unable to use it because they do not have the necessary enzyme, nitrogenase, to convert it into a form that they can use to make proteins.
• Soil bacteria, or rhizobia, are able to perform biological nitrogen fixation in which atmospheric nitrogen gas (N2) is converted into the ammonia (NH3) that plants are able to use to synthesize proteins.
• Both the plants and the bacteria benefit from the process of nitrogen fixation; the plant obtains the nitrogen it needs to synthesize proteins, while the bacteria obtain carbon from the plant and a secure environment to inhabit within the plant roots.
Key Terms
• rhizobia: any of various bacteria, of the genus Rhizobium, that form nodules on the roots of legumes and fix nitrogen
• nitrogen fixation: the conversion of atmospheric nitrogen into ammonia and organic derivatives, by natural means, especially by microorganisms in the soil, into a form that can be assimilated by plants
• nodule: structures that occur on the roots of plants that associate with symbiotic nitrogen-fixing bacteria
Nitrogen Fixation: Root and Bacteria Interactions
Nitrogen is an important macronutrient because it is part of nucleic acids and proteins. Atmospheric nitrogen, which is the diatomic molecule N2, or dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. However, plants cannot take advantage of this nitrogen because they do not have the necessary enzymes to convert it into biologically useful forms. However, nitrogen can be “fixed.” It can be converted to ammonia (NH3) through biological, physical, or chemical processes. Biological nitrogen fixation (BNF), the conversion of atmospheric nitrogen (N2) into ammonia (NH3), is exclusively carried out by prokaryotes, such as soil bacteria or cyanobacteria. Biological processes contribute 65 percent of the nitrogen used in agriculture.
The most important source of BNF is the symbiotic interaction between soil bacteria and legume plants, including many crops important to humans. The NH3 resulting from fixation can be transported into plant tissue and incorporated into amino acids, which are then made into plant proteins. Some legume seeds, such as soybeans and peanuts, contain high levels of protein and are among the most important agricultural sources of protein in the world.
Soil bacteria, collectively called rhizobia, symbiotically interact with legume roots to form specialized structures called nodules in which nitrogen fixation takes place. This process entails the reduction of atmospheric nitrogen to ammonia by means of the enzyme nitrogenase. Therefore, using rhizobia is a natural and environmentally-friendly way to fertilize plants as opposed to chemical fertilization that uses a non-renewable resource, such as natural gas. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen from the atmosphere. The process simultaneously contributes to soil fertility because the plant root system leaves behind some of the biologically-available nitrogen. As in any symbiosis, both organisms benefit from the interaction: the plant obtains ammonia and bacteria obtain carbon compounds generated through photosynthesis, as well as a protected niche in which to grow. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.02%3A_Soil_and_Plant_Microbiology/16.2G%3A_Nitrogen_Fixation-_Root_and_Bacteria_Interactions.txt |
The marine environment supplies many kinds of habitats that support marine life.
Learning Objectives
• Describe marine habitats
Key Points
• Marine habitats can be divided into coastal and open ocean habitats.
• Coastal habitats are found in the area that extends from as far as the tide comes in on the shoreline out to the edge of the continental shelf.
• Open ocean habitats are found in the deep ocean beyond the edge of the continental shelf.
• Most marine life is found in coastal habitats, even though the shelf area occupies only seven percent of the total ocean area.
Key Terms
• coastal: Relating to the coast; on or near the coast, as a coastal town, a coastal breeze.
• habitat: A specific place or natural conditions in which a plant or animal lives.
• marine: Of, or pertaining to, the sea (marine biology, marine insurance).
The marine environment supplies many kinds of habitats that support life. Marine life partially depends on the saltwater that is in the sea (“marine” comes from the Latin “mare,” meaning sea or ocean). A habitat is an ecological or environmental area inhabited by one or more living species.
Marine habitats can be divided into coastal and open ocean habitats. Coastal habitats are found in the area that extends from as far as the tide comes in on the shoreline, out to the edge of the continental shelf. Most marine life is found in coastal habitats, even though the shelf area occupies only seven percent of the total ocean area. Open ocean habitats are found in the deep ocean beyond the edge of the continental shelf.
Alternatively, marine habitats can be divided into pelagic and demersal habitats. Pelagic habitats are found near the surface or in the open water column, away from the bottom of the ocean. Demersal habitats are near or on the bottom of the ocean. An organism living in a pelagic habitat is said to be a pelagic organism, as in pelagic fish. Similarly, an organism living in a demersal habitat is said to be a demersal organism, as in demersal fish. Pelagic habitats are intrinsically shifting and ephemeral, depending on what ocean currents are doing.
Marine habitats can be modified by their inhabitants. Some marine organisms, like corals, kelp, mangroves and seagrasses, are ecosystem engineers, which reshape the marine environment to the point where they create habitats for other organisms.
Marine habitats include coastal zones, intertidal zones, sandy shores, rocky shores, mudflats, swamps and salt marshes, estuaries, kelp forests, seagrasses, and coral reefs. In addition, in the open ocean there are surface waters, deep sea and sea floor.
Intertidal zones (those areas close to shore) are constantly being exposed and covered by the ocean’s tides. A huge array of life lives within this zone.
Sandy shores, also called beaches, are coastal shorelines where sand accumulates. Waves and currents shift the sand, continually building and eroding the shoreline. Longshore currents flow parallel to the beaches, making waves break obliquely on the sand. These currents transport large amounts of sand along coasts, forming spits, barrier islands and tombolos. Longshore currents also commonly create offshore bars, which give beaches some stability by reducing erosion.
The relative solidity of rocky shores seems to give them a permanence compared to the shifting nature of sandy shores. This apparent stability is not real over even quite short geological time scales, but it is real enough over the short life of an organism. In contrast to sandy shores, plants and animals can anchor themselves to the rocks.
Mudflats are coastal wetlands that form when mud is deposited by tides or rivers. They are found in sheltered areas such as bays, bayous, lagoons, and estuaries. Mudflats may be viewed geologically as exposed layers of bay mud, resulting from deposition of estuarine silts, clays and marine animal detritus. Most of the sediment within a mudflat is within the intertidal zone, and thus the flat is submerged and exposed approximately twice daily.
Mangrove swamps and salt marshes form important coastal habitats in topical and temperate areas respectively. An estuary is a partly enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea.
Kelp forests are underwater areas with a high density of kelp. They are recognized as one of the most productive and dynamic ecosystems on Earth. Smaller areas of anchored kelp are called kelp beds. Kelp forests occur worldwide throughout temperate and polar coastal oceans.
Seagrasses are flowering plants from one of four plant families which grow in marine environments. They are called seagrasses because the leaves are long and narrow and are very often green, and because the plants often grow in large meadows, which look like grassland.
Reefs comprise some of the densest and most diverse habitats in the world. The best-known types of reefs are tropical coral reefs, which exist in most tropical waters; however, reefs can also exist in cold water. Reefs are built up by corals and other calcium-depositing animals, usually on top of a rocky outcrop on the ocean floor. Reefs can also grow on other surfaces; this has made it possible to create artificial reefs. Coral reefs also support a huge community of life, including the corals themselves, their symbiotic zooxanthellae, tropical fish, and many other organisms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3A%3A_Marine_Habitats.txt |
Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current.
Learning Objectives
• Recall Planktonic communities
Key Points
• Plankton are primarily divided into broad functional (or trophic level) groups: Phytoplankton, Zooplankton, and Bacterioplankton.
• Plankton cover a wide range of sizes, including microscopic to large organisms such as jellyfish.
• Plankton community into broad producer, consumer, and recycler groups.
Key Terms
• trophic: Describing the relationships between the feeding habits of organisms in a food chain.
• plankton: Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current. They provide a crucial source of food to many large aquatic organisms, such as fish and whales.
• organisms: An organism is any contiguous living system (such as animal, fungus, micro-organism, or plant). In at least some form, all types of organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole.
Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current. They provide a crucial source of food to many large aquatic organisms, such as fish and whales.
These organisms include drifting animals, plants, archaea, algae, or bacteria that inhabit the pelagic zone of oceans, seas, or bodies of fresh water. That is, plankton are defined by their ecological niche rather than phylogenetic or taxonomic classification.
Although many planktic (or planktonic) species are microscopic in size, plankton consists organisms covering a wide range of sizes, including large organisms such as jellyfish.
Plankton are primarily divided into broad functional (or trophic level) groups: Phytoplankton, Zooplankton, and Bacterioplankton.
Phytoplankton (from Greek phyton, or plant), autotrophic, prokaryotic, or eukaryotic algae live near the water surface where there is sufficient light to support photosynthesis. Among the more important groups are the diatoms, cyanobacteria, dinoflagellates, and coccolithophores.
Zooplankton (from Greek zoon, or animal), small protozoans or metazoans (e.g. crustaceans and other animals) that feed on other plankton and telonemia. Some of the eggs and larvae of larger animals, such as fish, crustaceans, and annelids, are included here.
Bacterioplankton, bacteria and archaea, which play an important role in remineralising organic material down the water column (note that the prokaryotic phytoplankton are also bacterioplankton).
This scheme divides the plankton community into broad producer, consumer, and recycler groups. However, determining the trophic level of some plankton is not straightforward. For example, although most dinoflagellates are either photosynthetic producers or heterotrophic consumers, many species are mixotrophic depending upon circumstances.
Aside from representing the bottom few levels of a food chain that supports commercially important fisheries, plankton ecosystems play a role in the biogeochemical cycles of many important chemical elements, including the ocean’s carbon cycle.
Primarily by grazing on phytoplankton, zooplankton provides carbon to the planktic foodweb, either respiring it to provide metabolic energy, or upon death as biomass or detritus. Typically more dense than seawater, organic material tends to sink. In open ocean ecosystems away from the coasts this transports carbon from surface waters to the deep. This process is known as the biological pump, and is one reason that oceans constitute the largest carbon sink on earth.
It might be possible to increase the ocean’s uptake of carbon dioxide generated through human activities by increasing plankton production through “seeding,” primarily with the micronutrient iron. However, this technique may not be practical at a large scale. Ocean oxygen depletion and resultant methane production (caused by the excess production remineralizing at depth) is one potential drawback.
The growth of phytoplankton populations is dependent on light levels and nutrient availability. The main factor limiting growth varies from region to region in the world’s oceans. On a broad scale, growth of phytoplankton in the oligotrophic tropical and subtropical gyres is generally limited by nutrient supply, while light often limits phytoplankton growth in subarctic gyres. Environmental variability at multiple scales influences the nutrient and light available for phytoplankton. As these organisms form the base of the marine food web, this variability in phytoplankton growth influences higher trophic levels. For example, at interannual scales phytoplankton levels temporarily plummet during El Nino periods, influencing populations of zooplankton, fishes, sea birds, and marine mammals.
The effects of anthropogenic warming on the global population of phytoplankton are an area of active research. Changes in the vertical stratification of the water column, the rate of temperature-dependent biological reactions, and the atmospheric supply of nutrients are expected to have important impacts on future phytoplankton productivity. Additionally, changes in the mortality of phytoplankton due to rates of zooplankton grazing may be significant.
Freshly hatched fish larvae are also plankton for a few days as long as they cannot swim against currents. Zooplankton are the initial prey item for almost all fish larvae as they switch from their yolk sacs to external feeding. Fish rely on the density and distribution of zooplankton to match that of new larvae, which can otherwise starve. Natural factors (e.g., current variations) and man-made factors (e.g. river dams) can strongly affect zooplankton, which can in turn strongly affect larval survival and therefore breeding success. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3B%3A_Planktonic_Communities.txt |
Plankton communities are divided into broad categories of producer, consumer, and recycler groups.
Learning Objectives
• Differentiate planktonic food webs
Key Points
• Plankton communities represent the bottom few levels of a food chain that supports commercially important fisheries.
• Plankton ecosystems also play a crucial role in the biogeochemical cycles of many important chemical elements, including the ocean’s carbon cycle.
• The growth of phytoplankton populations is dependent on light levels and nutrient availability.
Key Terms
• plankton: Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current. They provide a crucial source of food to many large aquatic organisms, such as fish and whales.
• ecosystems: Communities of living organisms (plants, animals and microbes) in conjunction with the nonliving components of their environment (things like air, water, and mineral soil), interacting as a system; linked together through nutrient cycles and energy flows.
• biogeochemical cycles: A biogeochemical cycle or substance turnover or cycling of substances is a pathway by which a chemical element or molecule moves through both biotic (biosphere) and abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. A cycle is a series of change which comes back to the starting point and which can be repeated.
Plankton communities are divided into broad categories of producer, consumer and recycler groups. However, determining the trophic level of some plankton is not straightforward. For example, although most dinoflagellates are either photosynthetic producers or heterotrophic consumers, many species are mixotrophic, depending upon circumstances.
Aside from representing the bottom few levels of a food chain that supports commercially important fisheries, plankton ecosystems play a role in the biogeochemical cycles of many important chemical elements, including the ocean’s carbon cycle.
Primarily by grazing on phytoplankton, zooplankton provide carbon to the planktic foodweb, either respiring it to provide metabolic energy, or upon death as biomass or detritus. Typically more dense than seawater, organic material tends to sink. In open-ocean ecosystems away from the coasts this transports carbon from surface waters to the deep. This process is known as the biological pump, and is one reason that oceans constitute the largest carbon sink on Earth.
It might be possible to increase the ocean’s uptake of carbon dioxide generated through human activities by increasing plankton production through “seeding”, primarily with the micronutrient iron. However, this technique may not be practical on a large scale. Ocean oxygen depletion and resultant methane production (caused by the excess production of remineralising at depth) is one potential drawback.
The growth of phytoplankton populations is dependent on light levels and nutrient availability. The chief factor limiting growth varies from region to region in the world’s oceans. On a broad scale, growth of phytoplankton in the oligotrophic tropical and subtropical gyres is generally limited by nutrient supply, while light often limits phytoplankton growth in subarctic gyres. Environmental variability at multiple scales influences the nutrient and light available for phytoplankton. As these organisms form the base of the marine food web, this variability in phytoplankton growth influences higher trophic levels. For example, at interannual scales phytoplankton levels temporarily plummet during El Nino periods, influencing populations of zooplankton, fish, sea birds, and marine mammals.
The effects of anthropogenic warming on the global population of phytoplankton is an area of active research. Changes in the vertical stratification of the water column, the rate of temperature-dependent biological reactions, and the atmospheric supply of nutrients are expected to have important impacts on future phytoplankton productivity. Additionally, changes in the mortality of phytoplankton due to rates of zooplankton grazing may be significant.
Freshly-hatched fish larvae are also plankton for a few days as long as they cannot swim against currents. Zooplankton are the initial prey item for almost all fish larvae as they switch from their yolk sacs to external feeding. Fish rely on the density and distribution of zooplankton to match that of new larvae, which can otherwise starve. Natural factors (e.g., current variations) and man-made factors (e.g. river dams) can strongly affect zooplankton, which can in turn strongly affect larval survival, and therefore breeding success. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3C%3A_Planktonic_Food_Webs.txt |
Ocean floor extremophile chemosynthetic microbes provide energy and carbon to the other organisms in these environments.
Learning Objectives
• Explain the importance of microbes and hydrothermal vents to underwater ecosystems
Key Points
• Recently, there has been the discovery of abundant marine life in the deep sea, especially around hydrothermal vents.
• Hydrothermal vents along the mid-ocean ridge spreading centers act as oases and support unique biomes and many new microbes.
• Each area of the seabed has typical features such as common soil composition, typical topography, salinity of water layers above it, marine life, magnetic direction of rocks, and sedimenting.
Key Terms
• plankton: Plankton (singular plankter) are any organisms that live in the water column and are incapable of swimming against a current. They provide a crucial source of food to many large aquatic organisms, such as fish and whales.
• ecosystems: Communities of living organisms (plants, animals and microbes) in conjunction with the nonliving components of their environment (things like air, water, and mineral soil), interacting as a system; linked together through nutrient cycles and energy flows.
• biogeochemical cycles: A biogeochemical cycle or substance turnover or cycling of substances is a pathway by which a chemical element or molecule moves through both biotic (biosphere) and abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. A cycle is a series of change which comes back to the starting point and which can be repeated.
Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet ‘s environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine.
Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other organisms, and these relationships affect the ecosystem. One example of these fundamental symbioses are chloroplasts, which allow eukaryotes to conduct photosynthesis. Chloroplasts are considered to be endosymbiotic cyanobacteria, a group of bacteria that are thought to be the origins of aerobic photosynthesis.
They are the backbone of all ecosystems, but even more so in the zones where light cannot approach and therefore photosynthesis cannot be the basic means to collect energy. In such zones, chemosynthetic microbes provide energy and carbon to the other organisms. Other microbes are decomposers, with the ability to recycle nutrients from other organisms’ waste poducts. These microbes play a vital role in biogeochemical cycles. The nitrogen cycle, the phosphorus cycle and the carbon cycle all depend on microorganisms in one way or another. For example, nitrogen which makes up 78% of the planet’s atmosphere is “indigestible” for most organisms, and the flow of nitrogen into the biosphere depends on a microbial process called fixation.
Recently there has been the discovery of abundant marine life in the deep sea, especially around hydrothermal vents. Large deep sea communities of marine life have been discovered around black and white smokers – hydrothermal vents emitting typical chemicals toxic to humans and most of the vertebrates. This marine life receives its energy from both the extreme temperature difference (typically a drop of 150 degrees) and from chemosynthesis by bacteria.
Brine pools are another seabed feature, usually connected to cold seeps. Hydrothermal vents along the mid-ocean ridge spreading centers act as oases, as do their opposites, cold seeps. Such places support unique biomes and many new microbes and other lifeforms have been discovered at these locations. The deepest recorded oceanic trench measured to date is the Mariana Trench, near the Philippines, in the Pacific Ocean at 10,924 m (35,838 ft). At such depths, water pressure is extreme. There is no sunlight, but some life still exists. A white flatfish, a shrimp, and a jellyfish were seen by the American crew of the bathyscaphe Trieste when it dove to the bottom in 1960. Marine life also flourishes around seamounts that rise from the depths, where fish and other sea life congregate to spawn and feed. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3D%3A_Ocean_Floor.txt |
A cold seep is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs.
Learning Objectives
• Outline the organisms that live in cold-seep ecosystems
Key Points
• Cold seeps develop unique topography over time, where reactions between methane and seawater create carbonate rock formations and reefs.
• Types of cold seeps can be distinguished according to the depth, as shallow cold seeps and deep cold seeps.
• Organisms living in cold seeps are known as extremophiles.
Key Terms
• cold seep: A cold seep (sometimes called a cold vent) is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs, often in the form of a brine pool. “Cold” does not mean temperature of seepage is lower than surrounding sea water. Actually, its temperature is often slightly higher.
• topography: A detailed graphic representation of the surface features of a place or object.
• extremophiles: An extremophile (from Latin extremus, meaning “extreme,” and Greek philiā (φ), meaning “love”) is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on earth.
A cold seep (sometimes called a cold vent) is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs, often in the form of a brine pool. “Cold” does not mean temperature of seepage is lower than surrounding sea water. Actually, its temperature is often slightly higher. Cold seeps constitute a biome supporting several endemic species.
Cold seeps develop unique topography over time, where reactions between methane and seawater create carbonate rock formations and reefs. These reactions may also be dependent on bacterial activity. Ikaite, a hydrous calcium carbonate, can be associated with oxidizing methane at cold seeps.
Types of cold seeps can be distinguished according to the depth, as shallow cold seeps and deep cold seeps. Cold seeps can also be distinguished in detail, as follows: oil/gas seeps, gas seeps, methane seeps, gas hydrate seeps, brine seeps, are forming brine pools, pockmarks and mud volcanos.
Organisms living in cold seeps are known as extremophiles. Biological research in cold seeps and hydrothermal vents has been mostly focused on the microbiology and the prominent chemosynthetic macro-invertebrates. Much less research has been done on the smaller benthic fraction at the size of the meiofauna (<1 mm).
Community composition’s orderly shift from one set of species to another is called ecological succession. The first type of organism to take advantage of this deep-sea energy source is bacteria. Aggregating into bacterial mats at cold seeps, these bacteria metabolize methane and hydrogen sulfide (another gas that emerges from seeps) for energy. This process of obtaining energy from chemicals is known as chemosynthesis.
During this initial stage, when methane is relatively abundant, dense mussel beds also form near the cold seep. Mostly composed of species in the genus Bathymodiolus, these mussels do not directly consume food. Instead, they are nourished by symbiotic bacteria that also produce energy from methane, similar to their relatives that form mats. Chemosynthetic bivalves are prominent constituents of the fauna of cold seeps and are represented in that setting by five families: Solemyidae, Lucinidae, Vesicomyidae, Thyasiridae, and Mytilidae.
This microbial activity produces calcium carbonate (CaCO3), which is deposited on the seafloor and forms a layer of rock. During a period lasting up to several decades, these rock formations attract siboglinid tubeworms, which settle and grow along with the mussels. Like the mussels, tubeworms rely on chemosynthetic bacteria (in this case, a type that needs hydrogen sulfide instead of methane) for survival. True to any symbiotic relationship, a tubeworm also provides for their bacteria by appropriating hydrogen sulfide from the environment. The sulfide not only comes from the water, but is also mined from the sediment through an extensive “root” system a tubeworm “bush” establishes in the hard, carbonate substrate. A tubeworm bush can contain hundreds of individual worms, which can grow a meter or more above the sediment.
Cold seeps do not last indefinitely. As the rate of gas seepage slowly decrease, the shorter-lived, methane-hungry mussels (or more precisely, their methane-hungry bacterial symbionts) start to die off. At this stage, tubeworms become the dominant organism in a seep community. As long as there is some sulfide in the sediment, the sulfide-mining tubeworms can persist. Individuals of one tubeworm species Lamellibrachia luymesi have been estimated to live for over 250 years in such conditions. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3E%3A_Cold-Seep_Ecosystems.txt |
A piezophile (also called a barophile) is an organism which thrives at high pressures, such as deep sea bacteria or archaea.
Learning Objectives
• Indicate how barophiles survive in the deep sea
Key Points
• The three main sources of energy and nutrients for deep sea communities are marine snow, whale falls, and chemosynthesis.
• Zones of the deep sea include the mesopelagic zone, the bathyal zone, the abyssal zone, and the hadal zone.
• Organisms have adapted in novel ways to become tolerant of the high pressures and cool temperatures in order to colonize deep sea habitats.
Key Terms
• deep sea: The deeper part of the sea or ocean in which no light penetrates.
• piezophile: A piezophile (also called a barophile) is an organism which thrives at high pressures, such as deep sea bacteria or archaea.
• chemosynthesis: The production of carbohydrates and other compounds from simple compounds such as carbon dioxide, using the oxidation of chemical nutrients as a source of energy rather than sunlight; it is limited to certain bacteria and fungi.
Deep sea communities currently remain largely unexplored, due the technological and logististical challenges, and the expense involved in visiting these remote biomes. Because of the unique challenges (particularly the high barometric pressure, extremes of temperature, and absence of light), it was long believed that little life existed in this hostile environment. Since the 19th century however, research has demonstrated that significant biodiversity exists in the deep sea.
The three main sources of energy and nutrients for deep sea communities are marine snow, whale falls, and chemosynthesis at hydrothermal vents and cold seeps.
Zones of the deep sea include the mesopelagic zone, the bathyal zone, the abyssal zone, and the hadal zone.
A piezophile, also called a barophile, is an organism which thrives at high pressures, such as deep sea bacteria or archaea. They are generally found on ocean floors, where pressure often exceeds 380 atm (38 MPa). Some have been found at the bottom of the Pacific Ocean where the maximum pressure is roughly 117 MPa. The high pressures experienced by these organisms can cause the normally fluid cell membrane to become waxy and relatively impermeable to nutrients. These organisms have adapted in novel ways to become tolerant of these pressures in order to colonize deep sea habitats. One example, xenophyophores, have been found in the deepest ocean trench, 6.6 miles (10,541 meters) below the surface.
Barotolerant bacteria are able to survive at high pressures, but can exist in less extreme environments as well. Obligate barophiles cannot survive outside of such environments. For example, the Halomonas species Halomonas salaria requires a pressure of 1000 atm (100 MPa) and a temperature of three degrees Celsius. Most piezophiles grow in darkness and are usually very UV-sensitive; they lack many mechanisms of DNA repair.
16.3G: Sea Coral and Sea Anemone Zooxanthellae
Zooxanthellae refers to a variety of species that form symbiotic relationships with other marine organisms, particularly coral.
Learning Objectives
• Outline the role Zooxanthellae play in animal sybiosis
Key Points
• Zooxanthellae species are members of the phylum Dinoflagellata. The most common genus is Symbiodinium.
• Each Symbiodinium cell is coccoid in hospite (living in a host cell) and surrounded by a membrane that originates from the host cell plasmalemma during phagocytosis.
• Zooxanthellates mutualistic relationships with reef-building corals form the basis of a highly diverse and productive ecosystem.
Key Terms
• endosymbiont: An organism that lives within the body or cells of another organism.
• phagocytosis: the process by which a cell incorporates foreign particles intracellularly.
• benthic: Pertaining to the benthos; living on the seafloor, as opposed to floating in the ocean.
Symbiodinium are colloquially called “zooxanthellae” (or “zoox”), and animals symbiotic with algae in this genus are said to be “zooxanthellate”. The term was loosely used to refer to any golden-brown endosymbionts, including diatoms and other dinoflagellates. The genus Symbiodinium encompasses the largest and most prevalent group of endosymbiotic dinoflagellates known to science. These unicellular algae commonly reside in the endoderm of tropical cnidarians such as corals, sea anemones, and jellyfish, where they translocate products of photosynthesis to the host and in turn receive inorganic nutrients (e.g. CO2, NH4+). They are also harbored by various species of sponges, flatworms, mollusks (e.g. giant clams), foraminifera (soritids), and some ciliates. Generally, these dinoflagellates enter the host cell through phagocytosis, persist as intracellular symbionts, reproduce, and disperse to the environment (note that in most mollusks, Symbiodinium are inter- rather than intra-cellular). Cnidarians that are associated with Symbiodinium occur mostly in warm oligotrophic (nutrient-poor) marine environments where they are often the dominant constituents of benthic communities. These dinoflagellates are therefore among the most abundant eukaryotic microbes found in coral reef ecosystems.
Symbiodinium are known primarily for their role as mutualistic endosymbionts. In hosts, they usually occur in high densities, ranging from hundreds of thousands to millions per square centimeter. The successful culturing of swimming gymnodinioid cells from coral led to the discovery that “zooxanthellae” were actually dinoflagellates. Each Symbiodinium cell is coccoid in hospite (living in a host cell) and surrounded by a membrane that originates from the host cell plasmalemma during phagocytosis. This membrane probably undergoes some modification to its protein content, which functions to limit or prevent phago-lysosome fusion. The vacuole structure containing the symbiont is therefore termed the symbiosome, and only a single symbiont cell is found within each symbiosome. It is unclear how this membrane expands to accommodate a dividing symbiont cell. Under normal conditions, symbiont and host cells exchange organic and inorganic molecules that enable the growth and proliferation of both partners. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3F%3A_The_Deep_Sea_and_Barophilism.txt |
Sponge reefs serve an important ecological function as habitat, breeding and nursery areas for fish and invertebrates.
Learning Objectives
• Compare the types of sponge communities
Key Points
• Sponge reefs are considered to be “living fossils”.
• Hexactinellids, or “glassy” sponges are characterized by a rigid framework of spicules made of silica.
• A unique feature of glassy sponges is that their tissues are made up almost entirely of syncytia.
Key Terms
• silica: Any of the silica group of the silicate minerals.
• Sponge reefs: Sponge reefs serve an important ecological function as habitat, breeding, and nursery areas for fish and invertebrates. The reefs are currently threatened by the fishery, offshore oil, and gas industries.
• syncytia: A syncytia (plural syncytia) is a multinucleate cell which can result from multiple cell fusions of uninuclear cells (i.e., cells with a single nucleus), in contrast to a coenocyte, which can result from multiple nuclear divisions without accompanying cytokinesis.
Sponge reefs serve an important ecological function as habitat, breeding, and nursery areas for fish and invertebrates. The reefs are currently threatened by the fishery, offshore oil, and gas industries. Attempts are being made to protect these unique ecosystems through fishery closures, and potentially the establishment of Marine Protected Areas (MAPs) around the sponge reefs.
Hexactinellids
Hexactinellid sponge reefs were common in the late Jurassic period, and were believed to have gone extinct during or shortly after the Cretaceous period. Living sponge reefs were discovered in the Queen Charlotte Basin (QCB) in 1987-1988, and were reported in the Georgia Basin (GB) in 2005. These sponge reefs are considered to be “living fossils. ”
Hexactinellids, or “glassy” sponges, are characterized by a rigid framework of spicules made of silica. Unlike other poriferans, hexactinellids do not possess the ability to contract. Another unique feature of glassy sponges is that their tissues are made up almost entirely of syncytia. In a syncytium there are many nuclei in a continuous cytoplasm; nuclei are not packaged in discrete cells.
As a result, the sponge has a distinctive electrical conduction system across its body. This allows the sponge to rapidly respond to disturbances, such as a physical impact or excessive sediment in the water. The sponge’s response is to stop feeding. It will try to resume feeding after 20-30 minutes, but will stop again if the irritation is still present.
Hexactinellids are exclusively marine and are found throughout the world in deep (>1000 m) oceans. Individual sponges grow at a rate of 0-7 cm/year, and can live to be at least 220 years old. Little is known about hexactinellid sponge reproduction. Like all poriferans, the hexactinellids are filter feeders. They obtain nutrition from direct absorption of dissolved substances, and to a lesser extent from particulate materials. There are no known predators of healthy reef sponges. This is likely because the sponges possess very little organic tissue; the siliceous skeleton accounts for 90% of the sponge body weight.
Hexasterophorans
Hexasterophoran sponges have spicules called hexactines that have six rays set at right angles. Orders within hexasterophora are classified by how tightly the spicules interlock with Lyssanctinosan spicules less tightly interlocked than those of Hexactinosan sponges.
The primary frame-building sponges are all members of the order Hexactinosa, and include the species Chonelasma/Heterochone calyx (chalice sponge), Aphrocallistes vastus (cloud sponge), and Farrea occa. Hexactinosan sponges have a rigid scaffolding of “fused” spicules that persists after the death of the sponge.
Lyssactinosa
Other sponge species abundant on sponge reefs are members of the order Lyssactinosa (Rosselid sponges) and include Rhabdocalyptus dawsoni (boot sponge), Acanthascus platei, Acanthascus cactus and Staurocalyptus dowlingi. Rosselid sponges have a “woven” or “loose” siliceous skeleton that does not persist after the death of the sponge, and are capable of forming mats, but not reefs.
Sponge Reefs
Each living sponge on the surface of the reef can be over 1.5 m tall. The reefs are composed of mounds called “bioherms” that are up to 21 m high, and sheets called “biostromes” that are 2-10 m thick, and may be many km wide. Each sponge in the order Hexactinosa has a rigid skeleton that persists after the death of the animal. This provides an excellent substrate for sponge larvae to settle upon, and new sponges grow on the framework of past generations. The growth of sponge reefs is thus analogous to that of coral reefs. The tendrils of new sponges wrap around spicules of older, deceased sponges. The tendrils will later form the basal plate of the adult sponge that firmly anchors the animal to the reef.
Deep ocean currents carry fine sediments that are captured by the scaffolding of sponge reefs. A sediment matrix of silt, clay, and some sand forms around the base of the sponge bioherms. The sediment matrix is soft near the surface, and firm below one metre deep. Dead sponges become covered in sediment, but do not lose their supportive siliceous skeleton. The sponge sediments have high levels of silica and organic carbon. The reefs grow parallel to the glacial troughs, and the morphology of reefs is due to deep currents.
Hexactinellids first appeared in the fossil record during the late Proterozoic, and the first Hexactinosans were found in the late Devonian. Hexactinellid sponge reefs were first identified in the middle Triassic (245-208 million years ago). The sponges reached their full extent in the late Jurassic (208-146 million years ago), when a discontinuous reef system 7,000 km long stretched across the northern Tethys and North Atlantic basins. This chain of sponge reefs is the largest known biostructure to have ever existed on Earth. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3H%3A_Sponge_Communities.txt |
Fresh water is naturally occurring water on Earth which has low concentrations of dissolved salts and other total dissolved solids.
Learning Objectives
• Generalize the characteristics of freshwater environments
Key Points
• Freshwater habitats are divided into lentic systems (which are the stillwaters including ponds, lakes, swamps and mires) and lotic systems, which are running water; and groundwater which flows in rocks and aquifers.
• Fresh water creates a hypotonic environment for aquatic organisms.
• Most aquatic organisms have a limited ability to regulate their osmotic balance and therefore can only live within a narrow range of salinity.
Key Terms
• hypotonic: Having a lower osmotic pressure than another.
• Freshwater: Fresh water is naturally occurring water on the Earth’s surface in ice sheets, ice caps, glaciers, bogs, ponds, lakes, rivers and streams, and underground as groundwater in aquifers and underground streams. Fresh water is generally characterized by having low concentrations of dissolved salts and other total dissolved solids.
• osmotic balance: Osmoregulation is the active regulation of the osmotic pressure of an organism’s fluids to maintain the homeostasis of the organism’s water content; that is, it keeps the organism’s fluids from becoming too diluted or too concentrated.
Fresh water is naturally occurring water on the Earth’s surface in ice sheets, ice caps, glaciers, bogs, ponds, lakes, rivers and streams, and underground as groundwater in aquifers and underground streams. Fresh water is generally characterized by having low concentrations of dissolved salts and other total dissolved solids. The term specifically excludes seawater and brackish water but it does include mineral rich waters such as chalybeate springs. The term “sweet water” has been used to describe fresh water in contrast to salt water.
Scientifically, freshwater habitats are divided into lentic systems, which are the stillwaters including ponds, lakes, swamps and mires; lotic systems, which are running water; and groundwater which flows in rocks and aquifers. There is, in addition, a zone which bridges between groundwater and lotic systems – the hyporheic zone – which underlies many larger rivers and can contain substantially more water than is seen in the open channel. It may also be in direct contact with the underlying underground water.
Fresh water creates a hypotonic environment for aquatic organisms. This is problematic for some organisms with pervious skins or with gill membranes, whose cell membranes may burst if excess water is not excreted. Some protists accomplish this using contractile vacuoles, while freshwater fish excrete excess water via the kidney. Although most aquatic organisms have a limited ability to regulate their osmotic balance and therefore can only live within a narrow range of salinity, diadromous fish have the ability to migrate between fresh water and saline water bodies. During these migrations they undergo changes to adapt to the surroundings of the changed salinities; these processes are hormonally controlled. The eel (Anguilla anguilla) uses the hormone prolactin, while in salmon (Salmo salar) the hormone cortisol plays a key role during this process.
Many sea birds have special glands at the base of the bill through which excess salt is excreted. Similarly the marine iguanas on the Galápagos Islands excrete excess salt through a nasal gland and they sneeze out a very salty excretion.
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• Visualisation of the distribution (by volume) of water on Earth.. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Water_d...stribution.svg. License: CC BY-SA: Attribution-ShareAlike | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.03%3A_Aquatic_Microbiology/16.3I%3A_Freshwater_Environments.txt |
Biogeochemical cycles are pathways by which essential elements flow from the abiotic and biotic compartments of the Earth.
Learning Objectives
• Identify sources and sinks of essential elements
Key Points
• Biogeochemical cycles are pathways by which nutrients flow between the abiotic and abiotic compartments of the Earth. The abiotic portion of the Earth includes the lithosphere (the geological component of the Earth) and the hydrosphere (the Earth’s water).
• Ecosystems rely on biogeochemical cycles. Many of the nutrients that living things depend on, such as carbon, nitrogen, and phosphorous are in constant circulation.
• Essential elements are often stored in reservoirs, where they can be taken out of circulation for years. For example, coal is a reservoir for carbon.
• Humans can affect biogeochemical cycles. Humans extract carbon and nitrogen from the geosphere and use them for energy and fertilizer. This has increased the amount of these elements in circulation, which has detrimental effects on ecosystems.
Key Terms
• Reservoir: Reservoirs are places where essential elements are sequestered for long periods of time.
• biogeochemical cycle: A pathway by which a chemical element or molecule moves through both biotic (biosphere) and abiotic (lithosphere, atmosphere, and hydropshere) compartments of the planet.
Most important substances on Earth, such as oxygen, nitrogen, and water undergo turnover or cycling through both the biotic (living) and abiotic (geological, atmospheric, and hydrologic) compartments of the Earth. Flows of nutrients from living to non-living components of the Earth are called biogeochemical cycles.
Nutrient Cycles and the Biosphere
Ecosystems hinge on biogeochemical cycles. The nitrogen cycle, the phosphorous cycle, the sulfur cycle, and the carbon cycle all involve assimilation of these nutrients into living things. These elements are transferred among living things through food webs, until organisms ultimately die and release them back into the geosphere.
Reservoirs of Essential Elements
Chemicals are sometimes sequestered for long periods of time and taken out of circulation. Locations where elements are stored for long periods of time are called reservoirs. Coal is a reservoir for carbon, and coal deposits can house carbon for thousands of years. The atmosphere is considered a reservoir for nitrogen.
Humans and Biogeochemical Cycles
Although the Earth receives energy from the Sun, the chemical composition of the planet is more or less fixed. Matter is occasionally added by meteorites, but supplies of essential elements generally do not change. However, human activity can change the proportion of nutrients that are in reservoirs and in circulation. For example, coal is a resevoir of carbon, but the human use of fossil fuels has released carbon into the atmosphere, increasing the amount of carbon in circulation. Likewise, phosphorous and nitrogen are extracted from geological reservoirs and used in phosphorous, and excesses of these elements have caused the overgrowth of plant matter and the disruption of many ecosystems.
16.4B: The Carbon Cycle
The carbon cycle describes the flow of carbon from the atmosphere to the marine and terrestrial biospheres, and the earth’s crust.
Learning Objectives
• Outline the flow of carbon through the biosphere and abiotic matter on earth
Key Points
• Atmospheric carbon is usually in the form of CO2. Carbon dioxide is converted to organic carbon through photosynthesis by primary producers such as plants, bacteria, and algae.
• Some organic carbon is returned to the atmosphere as CO2 during respiration. The rest of the organic carbon may cycle from organism to organism through the food chain. When an organism dies, it is decomposed by bacteria and its carbon is released into the atmosphere or the soil.
• Carbon is also found in the earth’s crust, primarily as limestone and kerogens.
Key Terms
• lithosphere: The rigid, mechanically strong, outer layer of the earth; divided into twelve major tectonic plates.
• chemoautotrophic: An organism obtaining its nutrition through the oxidation of non-organic compounds (or other chemical processes); as opposed to the process of photosynthesis.
• carbon cycle: The physical cycle of carbon through the Earth’s biosphere, geosphere, hydrosphere and atmosphere that includes such processes as photosynthesis, decomposition, respiration and carbonification.
The carbon cycle describes the flow of carbon between the biosphere, the geosphere, and the atmosphere, and is essential to maintaining life on earth.
Atmospheric Carbon Dioxide: Carbon in the earth’s atmosphere exists in two main forms: carbon dioxide and methane. Carbon dioxide leaves the atmosphere through photosynthesis, thus entering the terrestrial and marine biospheres. Carbon dioxide also dissolves directly from the atmosphere into bodies of water (oceans, lakes, etc.), as well as dissolving in precipitation as raindrops fall through the atmosphere. When dissolved in water, carbon dioxide reacts with water molecules and forms carbonic acid, which contributes to ocean acidity. Human activity over the past two centuries has significantly increased the amount of carbon in the atmosphere, mainly in the form of carbon dioxide, both by modifying ecosystems ‘ ability to extract carbon dioxide from the atmosphere and by emitting it directly, e.g. by burning fossil fuels and manufacturing concrete.
Terrestrial Biosphere: The terrestrial biosphere includes the organic carbon in all land-living organisms, both alive and dead, as well as carbon stored in soils. Although people often imagine plants as the most important part of the terrestrial carbon cycle, microorganisms such as single celled algae and chemoautotrophic bacteria are also important in converting atmospheric CO2 into terrestrial carbon. Carbon is incorporated into living things as part of organic molecules, either through photosynthesis or by animals that consume plants and algae. Some of the carbon in living things is released through respiration, while the rest remains in the tissue. Once organisms die, bacteria break down their tissues, releasing CO2 back into the atmosphere or into the soil.
Marine Biosphere: The carbon cycle in the marine biosphere is very similar to that in the terrestrial ecosystem. CO2 dissolves in the water and algae, plants and bacteria convert it into organic carbon. Carbon may transfer between organisms (from producers to consumers). Their tissues are ultimately broken down by bacteria and CO2 is released back into the ocean or atmosphere.
NASA | A Year in the Life of Earth’s CO2: An ultra-high-resolution NASA computer model has given scientists a stunning new look at how carbon dioxide in the atmosphere travels around the globe. Plumes of carbon dioxide in the simulation swirl and shift as winds disperse the greenhouse gas away from its sources. The simulation also illustrates differences in carbon dioxide levels in the northern and southern hemispheres and distinct swings in global carbon dioxide concentrations as the growth cycle of plants and trees changes with the seasons. The carbon dioxide visualization was produced by a computer model called GEOS-5, created by scientists at NASA Goddard Space Flight Center’s Global Modeling and Assimilation Office. The visualization is a product of a simulation called a “Nature Run.” The Nature Run ingests real data on atmospheric conditions and the emission of greenhouse gases and both natural and man-made particulates. The model is then left to run on its own and simulate the natural behavior of the Earth’s atmosphere. This Nature Run simulates January 2006 through December 2006. While Goddard scientists worked with a “beta” version of the Nature Run internally for several years, they released this updated, improved version to the scientific community for the first time in the fall of 2014.
Geologic Carbon: The earth’s crust also contains carbon. Much of the earth’s carbon is stored in the mantle, and has been there since the earth formed. Much of the carbon on the earth’s lithosphere (about 80%) is stored in limestone, which was formed from the calcium carbonate from the shells of marine animals. The rest of the carbon on the earth’s surface is stored in Kerogens, which were formed through the sedimentation and burial of terrestrial organisms under high heat and pressure. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.04%3A_Nutrient_Cycles/16.4A%3A_Sources_and_Sinks_of_Essential_Elements.txt |
Bacteria that perform anaerobic fermentation often partner with methanogenic archea bacteria to provide necessary products such as hydrogen.
Learning Objectives
• Assess syntrophy methanogenesis
Key Points
• Methanogenic bacteria are only found in the domain Archea, which are bacteria with no nucleus or other organelles.
• Methanogenesis is a form of respiration in which carbon rather than oxygen is used as an electron acceptor.
• Bacteria that perform anaerobic fermentation often partner with methanogenic bacteria. During anaerobic fermentation, large organic molecules are broken down into hydrogen and acetic acid, which can be used in methanogenic respiration.
• There are other examples of syntrophic relationships between methanogenic bacteria and mircoorganisms: protozoans in the guts of termites break down cellulose and produce hydrogen which can be used in methanogenesis.
Key Terms
• Archea: A domain of single-celled microorganisms. These microbes have no cell nucleus or any other membrane-bound organelles within their cells.
• syntrophy: A phenomenon where one species lives off the products of another species.
• methanogenesis: The generation of methane by anaerobic bacteria.
Syntrophy or cross feeding is when one species lives off the products of another species. A frequently cited example of syntrophy are methanogenic archaea bacteria and their partner bacteria that perform anaerobic fermentation.
Methanogenesis in microbes is a form of anaerobic respiration, performed by bacteria in the domain Archaea. Unlike other microorganisms, methanogens do not use oxygen to respire; but rather oxygen inhibits the growth of methanogens. In methanogenesis, carbon is used as the terminal electron receptor instead of oxygen. Although there are a variety of potential carbon based compounds that are used as electron receptors, the two best described pathways involve the use of carbon dioxide and acetic acid as terminal electron acceptors.
Acetic Acid: CO2+4H2→CH4+2H2OCO2+4H2→CH4+2H2O
Carbon Dioxide: CH3COOH→CH4+CO2CH3COOH→CH4+CO2
Many methanogenic bacteria that live in close association with bacteria produce fermentation products such as fatty acids longer than two carbon atoms, alcohols longer than one carbon atom, and branched chain and aromatic fatty acids. These products cannot be used in methanogenesis. Partner bacteria of the methanogenic archea therefore process these products. By oxydizing them to acetate, they allow them to be used in methanogenesis.
Methanogenic bacteria are important in the decomposition of biomass in most ecosystems. Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds that can be used in methanogenesis. The semi-final products of decay (hydrogen, small organics, and carbon dioxide) are then removed by methanogenesis. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.
Methanogenic archea bacteria can also form associations with other organisms. For example, they may also associate with protozoans living in the guts of termites. The protozoans break down the cellulose consumed by termites, and release hydrogen, which is then used in methanogenesis.
16.4D: The Phosphorus Cycle
Phosphorus, important for creating nucleotides and ATP, is assimilated by plants, then released through decomposition when they die.
Learning Objectives
• Explain the phosphorous cycle
Key Points
• Phosphorous is important for the production of ATP and nucleotides.
• Inorganic phosphorous is found in the soil or water. Plants and algae assimilate inorganic phosphorus into their cells, and transfer it to other animals that consume them.
• When organisms die, their phosphorous is released by decomposer bacteria.
• Aquatic phosphorous follows a seasonal cycle, inorganic phosphorous peaks in the spring causing rapid algae and plant growth, and then declines. As plants die, it is re-released into the water.
• Phosphorous based fertilizers can cause excessive algae growtin in aquatic systems, which can have negative impacts on the environment.
Key Terms
• hypertrophication: the ecosystem response to the addition of artificial or natural substances, such as nitrates and phosphates, through fertilizers or sewage, to an aquatic system. This response is usually an increase in primary production.
Phosphorus is an important element for living things because it is neccesary for nucleotides and ATP. Plants assimilate phosphorous from the environment and then convert it from inorganic phosphorous to organic phosphorous. Phosphorous can be transfered to other organisms when they consume the plants and algae. Animals either release phosphorous through urination or defecation, when they die and are broken down by bacteria. The organic phosphorous is released and converted back into inorganic phosphorous through decomposition. The phosphorous cycle differs from other nutrient cycles, because it never passes through a gaseous phase like the nitrogen or carbon cycles.
Phosphorous levels follow a seasonal pattern in aquatic ecosystems. In the spring, inorganic phosphorous is released from the sediment by convection currents in the warming water. When phosphorous levels are high, algae and plants reproduce rapidly. Much of the phosphorous is then converted to organic phosphorous, and primary productivity then declines. Later in the summer, the plants and algae begin to die off, and bacteria decompose them, and inorganic phosphorus is released back into the ecosystem. As phosphorous levels begin to increase at the end of the summer, primary plants and algae begin to rapidly grow again.
The phosphorous cycle is affected by human activities. Although phosphorous is normally a limiting nutrient, most agricultural fertilizers contain phosphorous. Run-off and drainage from farms can flood aquatic ecosystems with excess phosphorus. Artificial phosphorous can cause over growth of algae and plants in aquatic ecosytems. When the excess plant material is broken down, the decomposing bacteria can use up all the oxygen in the water causing dead zones. Most bodies of water gradually become more productive over time through the slow, natural accumulation of nutrients in a process called eutrophication. However, overgrowth of algae due to phosphorous fertilizer is called “cultural eutrophication” or “hypertrophication,” and is generally negative for ecosystems. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.04%3A_Nutrient_Cycles/16.4C%3A_Syntrophy_and_Methanogenesis.txt |
The nitrogen cycle is the process by which nitrogen is converted from organic to inorganic forms; many steps are performed by microbes.
Learning Objectives
• Describe the nitrogen cycle and how it is affected by human activity
Key Points
• Nitrogen is converted from atmospheric nitrogen (N2) into usable forms, such as NO2-, in a process known as fixation. The majority of nitrogen is fixed by bacteria, most of which are symbiotic with plants.
• Recently fixed ammonia is then converted to biologically useful forms by specialized bacteria. This occurs in two steps: first, bacteria convert ammonia in to (nitrites) NO2-, and then other bacteria species convert it to NO3- (nitrate).
• Nitriates are a form of nitrogen that is usable by plants. It is assimilated into plant tissue as protein. The nitrogen is passed through the food chain by animals that consume the plants, and then released into the soil by decomposer bacteria when they die.
• De-nitrifying bacteria convert NO2- back into atmospheric nitrogen (N2), completing the cycle.
Key Terms
• de-nitrification: A microbially facilitated process of nitrate reduction that may ultimately produce molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products.
• nitrification: The biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates.
• ammonification: The formation of ammonia or its compounds from nitrogenous compounds, especially as a result of bacterial decomposition.
The nitrogen cycle describes the conversion of nitrogen between different chemical forms. The majority of the earth’s atmosphere (about 78%) is composed of atmospheric nitrogen, but it is not in a form that is usable to living things. Complex species interactions allow organisms to convert nitrogen to usable forms and exchange it between themselves. Nitrogen is essential for the formation of amino acids and nucleotides. It is essential for all living things.
Fixation: In order for organisms to use atmospheric nitrogen (N2), it must be “fixed” or converted into ammonia (NH3). This can happen occasionally through a lightning strike, but the bulk of nitrogen fixation is done by free living or symbiotic bacteria. These bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia. It is then further converted by the bacteria to make their own organic compounds. Some nitrogen fixing bacteria live in the root nodules of legumes where they produce ammonia in exchange for sugars. Today, about 30% of the total fixed nitrogen is manufactured in chemical plants for fertilizer.
Nitrificaton: Nitrification is the conversion of ammonia (NH3) to nitrate (NO3). It is usually performed by soil living bacteria, such as nitrobacter. This is important because plants can assimilate nitrate into their tissues, and they rely on bacteria to convert it from ammonia to a usable form. Nitrification is performed mainly by the genus of bacteria, Nitrobacter.
Ammonification /Mineralization: In ammonification, bacteria or fungi convert the organic nitrogen from dead organisms back into ammonium (NH4+). Nitrification can also work on ammonium. It can either be cycled back into a plant usable form through nitrification or returned to the atmosphere through de-nitrification.
De-Nitrification: Nitrogen in its nitrate form (NO3) is converted back into atmospheric nitrogen gas (N2) by bacterial species such as Pseudomonas and Clostridium, usually in anaerobic conditions. These bacteria use nitrate as an electron acceptor instead of oxygen during respiration. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.04%3A_Nutrient_Cycles/16.4E%3A_The_Nitrogen_Cycle.txt |
Many bacteria can reduce sulfur in small amounts, but some bacteria can reduce sulfur in large amounts, in essence, breathing sulfur.
Learning Objectives
• Describe the sulfur cycle
Key Points
• The sulfur cycle describes the movement of sulfur through the geosphere and biosphere. Sulfur is released from rocks through weathering, and then assimilated by microbes and plants. It is then passed up the food chain and assimilated by plants and animals, and released when they decompose.
• Many bacteria can reduce sulfur in small amounts, but some specialized bacteria can perform respiration entirely using sulfur. They use sulfur or sulfate as an electron receptor in their respiration, and release sulfide as waste. This is a common form of anaerobic respiration in microbes.
• Sulfur reducing pathways are found in many pathogenic bacteria species. Tuberculosis and leprosy are both caused by bacterial species that reduce sulfur, so the sulfur reduction pathway is an important target of drug development.
Key Terms
• extremophile: An organism that lives under extreme conditions of temperature, salinity, and so on. They are commercially important as a source of enzymes that operate under similar conditions.
• assimilatory sulfate reduction: The reduction of 3′-Phosphoadenosine-5′-phosphosulfate, a more elaborated sulfateester, leads also to hydrogen sulfide, the product used in biosynthesis (e.g., for the production of cysteine because the sulfate sulfur is assimilated).
The Sulfur Cycle
The sulfur cycle describes the movement of sulfur through the atmosphere, mineral forms, and through living things. Although sulfur is primarily found in sedimentary rocks or sea water, it is particularly important to living things because it is a component of many proteins.
Sulfur is released from geologic sources through the weathering of rocks. Once sulfur is exposed to the air, it combines with oxygen, and becomes sulfate SO4. Plants and microbes assimilate sulfate and convert it into organic forms. As animals consume plants, the sulfur is moved through the food chain and released when organisms die and decompose.
Some bacteria – for example Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors. Others, such as Desulfuromonas, use only sulfur. These bacteria get their energy by reducing elemental sulfur to hydrogen sulfide. They may combine this reaction with the oxidation of acetate, succinate, or other organic compounds.
The most well known sulfur reducing bacteria are those in the domain Archea, which are some of the oldest forms of life on Earth. They are often extremophiles, living in hot springs and thermal vents where other organisms cannot live. Lots of bacteria reduce small amounts of sulfates to synthesize sulfur-containing cell components; this is known as assimilatory sulfate reduction. By contrast, the sulfate-reducing bacteria considered here reduce sulfate in large amounts to obtain energy and expel the resulting sulfide as waste. This process is known as dissimilatory sulfate reduction. In a sense, they breathe sulfate.
Sulfur metabolic pathways for bacteria have important medical implications. For example, Mycobacterium tuberculosis (the bacteria causing tuberculosis) and Mycobacterium leprae (which causes leoprosy) both utilize sulfur, so the sulfur pathway is a target of drug development to control these bacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.04%3A_Nutrient_Cycles/16.4F%3A_The_Sulfur_Cycle.txt |
Iron is an important limiting nutrient required for plants and animals; it cycles between living organisms and the geosphere.
Learning Objectives
• Compare the terrestrial and marine iron cycles
Key Points
• Iron is an important limiting nutrient for plants, which use it to produce chlorophyll. Photosynthesis depends on adequate iron supply. Plants assimilate iron from the soil into their roots.
• Animals consume plants and use the iron to produce hemoglobin, the oxygen transports protein found in red blood cells. When animals die, decomposing bacteria return iron to the soil.
• The marine iron cycle is very similar to the terrestrial iron cycle, except that phytoplankton and cyanobacteria assimilate iron.
• Iron fertilization has been studied as a method for sequestering carbon. Scientists have hoped that by adding iron to the ocean, plankton might be able to sequester the excess CO2 responsible for climate change. However, there is concern about the long term effects of this strategy.
Key Terms
• hemoglobin: the iron-containing oxygen transport metalloprotein in the red blood cells of all vertebrates
Iron (Fe) follows a geochemical cycle like many other nutrients. Iron is typically released into the soil or into the ocean through the weathering of rocks or through volcanic eruptions.
The Terrestrial Iron Cycle: In terrestrial ecosystems, plants first absorb iron through their roots from the soil. Iron is required to produce chlorophyl, and plants require sufficient iron to perform photosynthesis. Animals acquire iron when they consume plants, and iron is utilized by vertebrates in hemoglobin, the oxygen-binding protein found in red blood cells. Animals lacking in iron often become anemic and cannot transmit adequate oxygen. Bacteria then release iron back into the soil when they decompose animal tissue.
The Marine Iron Cycle: The oceanic iron cycle is similar to the terrestrial iron cycle, except that the primary producers that absorb iron are typically phytoplankton or cyanobacteria. Iron is then assimilated by consumers when they eat the bacteria or plankton. The role of iron in ocean ecosystems was first discovered when English biologist Joseph Hart noticed “desolate zones,” which are regions that lacked plankton but were rich in nutrients. He hypothesized that iron was the limiting nutrient in these areas. In the past three decades there has been research into using iron fertilization to promote alagal growth in the world’s oceans. Scientists hoped that by adding iron to ocean ecosystems, plants might grown and sequester atmospheric CO2. Iron fertilization was thought to be a possible method for removing the excess CO2 responsible for climate change. Thus far, the results of iron fertilization experiments have been mixed, and there is concern among scientists about the possible consequences of tampering nutrient cycles.
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Symbiosis is a relationship between two organisms: it can be mutualistic (both benefit), commensal (one benefits), or parasitic.
Learning Objectives
• Compare Mutualism and Symbiosis
Key Points
• Mutualism, a relationship in which both species benefit, is common in nature. In microbiology, there are many examples of mutualistic bacteria in the gut that aid digestion in both humans and animals.
• Commensalism is a relationship between species in which one benefits and the other is unaffected. Humans are host to a variety of commensal bacteria in their bodies that do not harm them but rely on them for survival (e.g. bacteria that consume dead skin).
• Parasitic relationships, in which one species benefits and the other suffers, are very common in nature. Most of the microorganisms studied in medical microbiology are parasitic and feed on human tissue. For example, cholera, leshmaniasis, and Giardia are all parasitic microbes.
• Symbiotic relationships can also be classified by the physical relationship between the two species. Endosymbionts live inside the tissues of the host, while ectosymbionts live outside of their partner species.
Key Terms
• commensalism: A class of relationship between two organisms in which one organism benefits without affecting the other
• symbiosis: A close and often long-term interaction between two or more different biological species
• mutualism: A relationship between individuals of different species in which both individuals benefit
Symbiosis is any relationship between two or more biological species. Such relationships are usually long term and have a strong impact on the fitness of one or both organisms. Symbiotic relationships are categorized by the benefits and physical relationships experienced by each species.
Common types of symbiosis are categorized by the degree to which each species benefits from the interaction:
• Mutualism: In mutualistic interactions, both species benefit from the interaction. A classic example of mutualism is the relationship between insects that pollinate plants and the plants that provide those insects with nectar or pollen. Another classic example is the behavior of mutualistic bacteria in ecology and human health. Gut bacteria in particular are very important for digestion in humans and other species. In humans, gut bacteria assist in breaking down additional carbohydrates, out-competing harmful bacteria, and producing hormones to direct fat storage. Humans lacking healthy mutualistic gut flora can suffer a variety of diseases, such as irritable bowel syndrome. Some ruminant animals, like cows or deer, rely on special mutualistic bacteria to help them break down the tough cellulose in the plants they eat. In return, the bacteria get a steady supply of food.
• Commensalism: In commensalism, one organism benefits while the other organism neither benefits nor suffers from the interaction. For example, a spider may build a web on a plant and benefit substantially, while the plant remains unaffected. Similarly, a clown fish might live inside a sea anemone and receive protection from predators, while the anemone neither benefits nor suffers.
• Parasitism: Parasites are organisms that harm their symbiotic partners. Parasitism is incredibly common in nature: depending on the definition, more than half of all species may go through at least one parasitic stage in their life cycle. There are many well-documented examples of parasitic bacteria and microorganisms throughout this text.
Symbiosis can also be characterized by an organism’s physical relationship with its partner.
• Endosymbiosis: a relationship in which one of the symbiotic species lives inside the tissue the other. For example, Coral polyps have special algae called zooxanthelle that live inside their cells. Zooxanthelle provide sugars to the coral through photosynthesis. Similarly, nitrogen-fixing fungi often live inside the cells of plants, providing nitrogen in exchange for the sugars of photosynthesis.
• Ectosymbiosis: a relationship in which one species lives on the outside surface of the other. Barnacles that live on whales and bromeliads that live on tropical trees are examples of endosymbionts.
These categories can be paired with the above terms to better describe the species’ interactions. For example, you might say that a gut bacteria is an “endosymbiotic mutualist,” or that a flea is an “ectosymbiotic parasite. ” | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.05%3A_Microbial_Symbioses/16.5A%3A_Mutualism_vs._Symbiosis.txt |
Ruminant animals (such as deer and cows) digest food in a four-chambered stomach with the help of special bacteria, protozoa, and fungi.
Learning Objectives
• Identify how ruminant animals host symbiotic bacteria
Key Points
• Ruminant animals use a special four-chambered stomach with a unique microbial flora to digest tough cellulose found in the plants in their diets. Most vertebrates cannot make cellulase, the enzyme that breaks down cellulose, but microbes in the rumen produce it for them.
• Ruminants chew and ingest plant matter and then swallow it. The plant matter is separated into liquids and solids in the rumen, and liquids drain into the reticulum. Solids in the rumen are then regurgitated into the mouth to be chewed and further broken down.
• Liquids pass from the reticulum into the omasum, where sugars, fatty acids, and other nutrients are absorbed into the blood stream.
• After the omasum, food passes into the abomasum, which is much like the stomach in non-ruminant (monogastric) animals, and from there moves into the small intestine, where it is digested.
Key Terms
• Rumen: The first chamber in the alimentary canal of ruminant animals. It serves as the primary site for microbial fermentation of ingested feed.
• Abomasum: The fourth and final stomach compartment in ruminants. It secretes rennin – the artificial form of which is called rennet, and is used in cheese creation.
• Omasum: The third compartment of the stomach in ruminants. Though its functions have not been well-studied, it appears to primarily aid in the absorption of water, magnesium, and the volatile fatty acids produced.
A Ruminant’s Multi-chambered Stomach
Ruminants are mammals that digest plant based food by processing it in a series of chambers in their stomachs. There are about 150 species of ruminants, including both domestic and wild species. Ruminating mammals include cattle, goats, sheep, giraffes, bison, moose, elk, yaks, water buffalo, deer, camels, alpacas, llamas, and antelope.
Ruminants differ from non-ruminants (called monogastrics) because they have a four-chambered stomach. The four compartments are called the rumen, the reticulum, the omasum, and the abomasum. The rumen and the reticulum are connected and work in concert and are therefore sometimes called the “reticulorumen”.
The Ruminant Digestive Process
• Ruminants chew plant matter to mix it with saliva and swallow. The food then enters the first two stomach chambers, the reticulum and rumen (or reticulorumen).
• The reticulum and rumen work together to separate solids and liquids. Contractions push solid food particles back up into the rumen, while liquids are drained into the reticulum. Specialized microbe species live in the rumen and help ruminants break down cellulose.
• Solids are formed into a bolus, called “cud,” in the rumen and the solid cud is regurgitated back up to the mouth where it is chewed a second time, and returned to the reticulorumen to repeat the process.
• Liquid digesta in the reticulum is passed into the omasum where nutrients and water are absorbed into the blood stream.
• After this, digesta is passed into the abomasum, which is similar to the stomach of other animals. After the abomasum, digesta moves through the large and small intestines.
Ruminants are of interest to microbiologists because they have unique species of bacteria, yeasts, protozoa, and fungi in their rumens. The plant matter consumed by ruminants is high in cellulose, but vertebrates cannot produce cellulase which is the enzyme required to break down cellulose. Thus ruminants depend on the symbiotic microbes in their guts to break down cellulose for digestion. There is no oxygen in the rumen, so bacteria in the rumen are typically anaerobes or facultative anaerobes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.05%3A_Microbial_Symbioses/16.5B%3A_The_Rumen_and_Ruminant_Animals.txt |
Hydrothermal vents are home to chemosynthetic bacteria, which are the basis of a unique ecosystem that thrives in total darkness.
Learning Objectives
• Describe hydrothermal vent microbial ecosystems
Key Points
• Hydrothermal vents emit nutrient rich, geothermally heated water. Mats of chemosynthetic bacteria grow around the vents and synthesize carbohydrates from the carbon dioxide ejected by the vent.
• Many species of crabs, worms, snails, and tube worms depend on these bacterial mats for food. These species are often specially adapted to life in the lightless, high pressure, and hot environment of the vent.
• Vents are the target of exploitation of the mining industry, which is a cause for concern among marine biologists. Mining could damage these very unique and diverse ecosystems.
Key Terms
• chemosynthesis: The production of carbohydrates and other compounds from simple compounds such as carbon dioxide, using the oxidation of chemical nutrients as a source of energy rather than sunlight; it is limited to certain bacteria and fungi.
• geothermal: Pertaining to heat energy extracted from reservoirs in the earth’s interior.
Hydrothermal Vents and Their Microbial Communities
A hydrothermal vent is a fissure in the earth’s surface from which geothermally heated water issues. They are typically found deep below the surface of the ocean. Hydrothermal vents are of interest to microbiologists because they have unique microbial communities found nowhere else on earth.
In most shallow water and terrestrial ecosystems, energy comes from sunlight, but in the deep ocean there is total darkness. However, hydrothermal vents often expel nutrient rich water, containing methane and sulfur compounds. Vent bacteria can synthesize all the compounds they need to live from these nutrients, a process called chemosynthesis. These bacteria form the basis of the entire hydrothermal vent ecosystem.
The chemosynthetic bacteria grow into a thick mat, covering the hydrothermal vent, and this is the first trophic level of the ecosystem. Snails, shrimp crabs, tube worms, and fish feed on the bacterial mat and attract larger organisms such as squid and octopuses. Many of these species are specially adapted to live in the dark and lack eyes. Hydrothermal vents are biodiversity hot spots because they have many species that are uniquely adapted to live in this harsh environment. For example, the Pompeii tube worm Alvinella pompejana can resist temperatures up to 176°F. These ecosystems are almost entirely independent of sunlight (although the dissolved oxygen used by some animals does ultimately come from plants at the surface ).
Despite being some of the most remote ecosystems in the world, hydrothermal vents are under threat from mining companies. As mineral resources on land have become depleted, mining companies have turned to deep sea geothermal vents to extract metals and sulfur. Although the technology for deep sea mining is new, conservation biologists are concerned that mining hydrothermal vents will destroy these fragile and unique ecosystems.
16.5D: Squid-Aliivibrio Symbiosis
Squid host light-generating Allivibiro bacteria in a special organ so that they can illuminate themselves and blend in with the environment.
Learning Objectives
• Explain the symbiotic relationship of squid and aliivibrio
Key Points
• Squid rely on Allivibrio bacteria to generate light that allows them to blend in with the light coming from above. Animals below them cannot see their shadow when they view the squid from below.
• Squid use mucus to attract many species of bacteria into their light organ, but they sort out Aliivibiro in several ways. Ciliated cells in the light organ create a current that expels most bacteria, and the squid uses hydrogen peroxide to create a hostile environment that Aliivibrio can resist.
• Once inside the light organ, the Aliivibrio bacteria receive sugars and amino acids from the squid. However, this is costly to the squid, and the squid clears out its light organ during the day so that it does not have to constantly maintain a colony of Aliivibrio bacteria.
Key Terms
• cilia: Organelles found in eukaryotic cells. Cilia are slender protuberances that project from the much larger cell body.
• BIoluminescence: The emission of light by a living organism.
Bioluminescence
A special category of symbiotic relationships involve bioluminescence, where light producing bacteria are hosted by another organism. One of the best studied examples of bioluminescence is the Hawaiian bobtail squid (Euprymna scolopes) and its mutualistic bacteria, Aliivibrio fischeri. Aliivibrio fischeri inhabits a special light organ in the squid’s mantle. The bacteria are fed a sugar and amino acid solution by the squid. In return, they produce light to hide the squid’s silhouette when viewed from below, allowing the squid to match ambient light conditions.
Bobtail squid hatchlings do not have Aliivibrio fischeri naturally in their bodies. They are born with a special light organ structure, with cilliated cells at the opening designed to trap passing A. fischeri, but must obtain the bacteria from sea water. To do this, the squid secretes a special mucus whenever its cells detect peptidoglycan (which is found in the cell walls of bacteria). The mucus collects near the opening of the light organ which traps passing bacteria. The squid weeds out unwanted bacteria in several ways. For instance, A. fischeri is able to survive in the mucus better than other species. It is also a very mobile bacteria, and is able to swim against the current created by the cilia at the mouth of the light organ.
The squid also creates a hostile environment at the entrance to the light organ by secreting an enzyme that splits hydrogen peroxide, creating a toxic environment for most bacteria. Aliivibrio fischeri can capture hydrogen peroxide before the squid can use it as a toxin, and thus can survive in the hostile chemical environment. Once A. fischeri has passed these hurdles at the opening of the light organ, it can colonize chambers of the light organ and begin enjoying the benefits of symbiosis.
Despite all the effort that goes into obtaining Aliivibrio fischeri, the squid ejects 95% of its bacteria every day. It not fully understood why the squid cleans out its light organ, but the bacteria require a great deal of sugar and amino acids, so it may be most useful to the squid to host bacteria only when they are needed. It may also provide a supply of bacteria for squid hatchlings. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.05%3A_Microbial_Symbioses/16.5C%3A_Hydrothermal_Vent_Microbial_Ecosystems.txt |
Members of Kingdom Fungi form ecologically beneficial mutualistic relationships with cyanobateria, plants, and animals.
Learning Objectives
• Describe mutualistic relationships with fungi
Key Points
• Mutualistic relationships are those where both members of an association benefit; Fungi form these types of relationships with various other Kingdoms of life.
• Mycorrhiza, formed from an association between plant roots and primitive fungi, help increase a plant’s nutrient uptake; in return, the plant supplies the fungi with photosynthesis products for their metabolic use.
• In lichen, fungi live in close proximity with photosynthetic cyanobateria; the algae provide fungi with carbon and energy while the fungi supplies minerals and protection to the algae.
• Mutualistic relationships between fungi and animals involves numerous insects; Arthropods depend on fungi for protection, while fungi receive nutrients in return and ensure a way to disseminate the spores into new environments.
Key Terms
• mycorrhiza: a symbiotic association between a fungus and the roots of a vascular plant
• lichen: any of many symbiotic organisms, being associations of fungi and algae; often found as white or yellow patches on old walls, etc.
• thallus: vegetative body of a fungus
Mutualistic Relationships
Symbiosis is the ecological interaction between two organisms that live together. However, the definition does not describe the quality of the interaction. When both members of the association benefit, the symbiotic relationship is called mutualistic. Fungi form mutualistic associations with many types of organisms, including cyanobacteria, plants, and animals.
Fungi & Plant Mutualism
Mycorrhiza, which comes from the Greek words “myco” meaning fungus and “rhizo” meaning root, refers to the association between vascular plant roots and their symbiotic fungi. About 90 percent of all plant species have mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area in contact with the soil to channel water and minerals from the soil into the plant, thereby increasing a plant’s nutrient uptake. In exchange, the plant supplies the products of photosynthesis to fuel the metabolism of the fungus.
Mycorrhizae display many characteristics of primitive fungi: they produce simple spores, show little diversification, do not have a sexual reproductive cycle, and cannot live outside of a mycorrhizal association. There are a number of types of mycorrhizae. Ectomycorrhizae (“outside” mycorrhiza) depend on fungi enveloping the roots in a sheath (called a mantle) and a Hartig net of hyphae that extends into the roots between cells. The fungal partner can belong to the Ascomycota, Basidiomycota, or Zygomycota. In a second type, the Glomeromycete fungi form vesicular–arbuscular interactions with arbuscular mycorrhiza (sometimes called endomycorrhizae). In these mycorrhiza, the fungi form arbuscules that penetrate root cells and are the site of the metabolic exchanges between the fungus and the host plant. The arbuscules (from the Latin for “little trees”) have a shrub-like appearance. Orchids rely on a third type of mycorrhiza. Orchids are epiphytes that form small seeds without much storage to sustain germination and growth. Their seeds will not germinate without a mycorrhizal partner (usually a Basidiomycete). After nutrients in the seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates and minerals. Some orchids continue to be mycorrhizal throughout their lifecycle.
Lichens
Lichens display a range of colors and textures. They can survive in the most unusual and hostile habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot penetrate. Lichens can survive extended periods of drought: they become completely desiccated and then rapidly become active once water is available again. Lichens fulfill many ecological roles, including acting as indicator species, which allow scientists to track the health of a habitat because of their sensitivity to air pollution.
Lichens are not a single organism, but, rather, an example of a mutualism in which a fungus (usually a member of the Ascomycota or Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a prokaryotic cyanobacterium). Generally, neither the fungus nor the photosynthetic organism can survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also attaches the symbiotic organism to the substrate.
The thallus of lichens grows very slowly, expanding its diameter a few millimeters per year. Both the fungus and the alga participate in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens.
Fungi & Animal Mutualism
Fungi have evolved mutualisms with numerous insects. Arthropods (jointed, legged invertebrates, such as insects) depend on the fungus for protection from predators and pathogens, while the fungus obtains nutrients and a way to disseminate spores into new environments. The association between species of Basidiomycota and scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally farm fungi. They cut disks of leaves from plants and pile them up in gardens. Fungi are cultivated in these disk gardens, digesting the cellulose in the leaves that the ants cannot break down. Once smaller sugar molecules are produced and consumed by the fungi, the fungi in turn become a meal for the ants. The insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they cultivate.
16.5F: Agrobacterium and Crown Gall Disease
Argobacterium causes Crown Gall Disease by transferring a DNA plasmid to the host plant, causing the host to make nutrients for it.
Learning Objectives
• Summarize the symbiotic relationship between plants and agrobacterium
Key Points
• Crown Gall Disease is caused by Agrobacterium tumefaciens, a bacteria that infects plants. The bacteria causes tumors on the stem of its host.
• Agrobacterium tumefaciens manipulates its hosts by transferring a DNA plasmid to the cells of its host. Plasmids are normally used to transfer DNA from bacteria to bacteria.
• Once in the host cell, the plasmid integrates itself into the host plant cell’s genome and forces the host to produce unique amino acids and other substances which nourish the bacteria. These compounds are unusable by most bacteria, so Argobacteria can out-compete other species.
Key Terms
• plasmid: A circle of double-stranded DNA that is separate from the chromosomes, which is found in bacteria and protozoa.
• pilus: A hair-like appendage found on the cell surface of many bacteria.
Crown Gall Disease is caused by a bacteria called Agrobacterium tumefaciens. The disease manifests as a tumor-like growth usually at the junction of the root and shoot. A. tumefaciens can transfer part of its DNA to the host plant, through a plasmid – a bacterial DNA molecule that is independent of a chromosome. The new DNA segment causes the plant to produce unusual amino acids and plant hormones which provide the bacteria with carbon and nitrogen.
Bacteria normally use plasmids for horizontal gene transfer, so they can share genes with related bacteria to help them cope with stressful environments. For example, plasmids can confer on bacteria the ability to fix nitrogen, or to resist antibiotic compounds. Typically bacteria transfer plasmids through conjugation: a donor bacteria creates a tube called a pilus that penetrates the cell wall of the recipient bacteria and the plasmid DNA passes through the tube. The other bacteria either integrates the plasmid into its chromosomes, or it remains free-floating in the cytoplasm. In either case, the recipient bacteria receives new genetic material.
In the case of Crown Gall Disease, A. tumefaciens transfers a plasmid containing T-DNA into the cells of its host plant through conjugation, as it would with another bacteria. However, once inside the plant cell, the DNA integrates semi-randomly into the genome of the plant and changes the behavior of the celll.
The new plasmid genes are expressed by the plant cells, and cause them to secrete enzymes that produce the amino acids octopine or nopaline. It also carries genes for the biosynthesis of the plant hormones, auxin and cytokinins, and for the biosynthesis of opines, providing a carbon and nitrogen source for the bacteria.
These opines can be used by very few other bacteria and give A. tumefaciens a competitive advantage. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.05%3A_Microbial_Symbioses/16.5E%3A_Mutualistic_Relationships_with_Fungi_and_Fungivores.txt |
Legumes have a symbiotic relationship with bacteria called rhizobia, which create ammonia from atmospheric nitrogen and help the plant.
Learning Objectives
• Evaluate legume and nitrogen-fixing bacteria symbiosis
Key Points
• Rhizobia normally live in the soil, but when there is limited soil nitrogen, legumes release flavonoids which signal to rhizobia that the plant is seeking symbiotic bacteria.
• When exposed to flavonoids, the Rhizobia release nodulation factor, which stimulates the plant to create deformed root hairs. Rhizobia then form an ” infection thread” which allows them to enter the root cells through the root hairs.
• Once the rhizobia are inside the root cells, the root cells divide rapidly, forming a nodule.
• The rhizobia create ammonia from nitrogen in the air, which is used by the plant to create amino acids and nucleotides. The plant provides the bacteria with sugars.
Key Terms
• Nodulation Factor: Signaling molecules produced by bacteria known as rhizobia during the initiation of nodules on the root of legumes. A symbiosis is formed when legumes take up the bacteria.
Legumes and their Nitrogen-Fixing Bacteria
Many legumes have root nodules that provide a home for symbiotic nitrogen-fixing bacteria called rhizobia. This relationship is particularly common in nitrogen-limited conditions. The Rhizobia convert nitrogen gas from the atmosphere into ammonia, which is then used in the formation of amino acids and nucleotides.
Rhizobia normally live in the soil and can exist without a host plant. However, when legume plants encounter low nitrogen conditions and want to form a symbiotic relationship with rhizobia they release flavinoids into the soil. Rhizobia respond by releasing nodulation factor (sometimes just called nod factor), which stimulates nodule formation in plant roots. Exposure to nod factor triggers the formation of deformed root hairs, which permit rhizobia to enter the plant. Rhizobia then form an infection thread, which is an intercellular tube that penetrates the cells of the host plant, and the bacteria then enter the host plants cells through the deformed root hair. Rhizobia can also enter the root by inserting themselves between cracks between root cells; this method of infection is called crack entry. Bacteria enter the root cells from the intercellular spaces, also using an infection thread to penetrate cell walls. Infection triggers rapid cell division in the root cells, forming a nodule of tissue.
The relationship between a host legume and the rhizobia is symbiotic, providing benefits to both participants. Once the rhizobia have established themselves in the root nodule, the plant provides carbohydrates in the form of malate and succinate, and the rhizobia provide ammonia for the formation of amino acids. Many legumes are popular agricultural crops specifically because they require very little fertilizer: their rhiziobia fix nitrogen for them. Used properly some legumes can even serve as fertilizer for later crops, binding nitrogen in the plant remains in the soil.
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Microbial ore leaching is the process in which microorganisms are used to extract metals from ores.
Learning Objectives
• Assess the advantages of microbial ore leaching
Key Points
• Bioleaching is cheaper than chemical extraction, safer for the environment, and more efficient in extracting metals with low concentration in ores.
• It is performed by iron and sulfide oxidizing bacteria or acid producing fungus.
• Bacteria recycle the major leaching reagent, like ferric iron, and perform further oxidation steps while gaining energy from the electron transfer.
Key Terms
• ore leaching: The process of recovering metals from ores by using a number of different techniques.
Microbial ore leaching (bioleaching) is the process of extracting metals from ores with the use of microorganisms. This method is used to recover many different precious metals like copper, lead, zinc, gold, silver, and nickel. Microorganisms are used because they can:
• lower the production costs.
• cause less environmental pollution in comparison to the traditional leaching methods.
• very efficiently extract metals when their concentration in the ore is low.
The Leaching Process
Bacteria perform the key reaction of regenerating the major ore oxidizer which in most cases is ferric iron as well as further ore oxidation. The reaction is performed at the bacterial cell membrane. In the process, free electrons are generated and used for the reduction of oxygen to water which produces energy in the bacterial cell.
Ores, like pyrite (FeS2), are first oxidized by ferric iron (Fe3+) to thiosulfate (S2O32-) in the absence of bacteria.
In the first step, disulfide is spontaneously oxidized to thiosulfate by ferric iron (Fe3+), which in turn is reduced to give ferrous iron (Fe2+):
(1) FeS2+6Fe3++3H2O⟶7Fe2++S2O2−3+6H+spontaneousFeS2+6Fe3++3H2O⟶7Fe2++S2O32−+6H+spontaneous
Bacteria are added in the second step and recover Fe3+ from ferrous iron (Fe2+) which is then reused in the first step of leaching:
(2) 4Fe2++O2+4H+⟶4Fe3++2H2O(iron oxidizers)4Fe2++O2+4H+⟶4Fe3++2H2O(iron oxidizers)
Thiosulfate is also oxidized by bacteria to give sulfate:
(3) S2O2−3+2O2+H2O⟶2SO2−4+2H+(sulfur oxidizers)S2O32−+2O2+H2O⟶2SO42−+2H+(sulfur oxidizers)
The ferric iron produced in reaction (2) oxidized more sulfide as in reaction (1), closing the cycle and given the net reaction:
(4) 2FeS2+7O2+2H2O⟶2Fe2++4SO2−4+4H+2FeS2+7O2+2H2O⟶2Fe2++4SO42−+4H+
The net products of the reaction are soluble ferrous sulfate and sulfuric acid.
The microbial oxidation process occurs at the cell membrane of the bacteria. The electrons pass into the cells and are used in biochemical processes to produce energy for the bacteria while reducing oxygen to water. The critical reaction is the oxidation of sulfide by ferric iron. The main role of the bacterial step is the regeneration of this reactant.
Copper leaching has a very similar mechanism.
Microorganisms Capable of Ore Leaching
Bioleaching reactions industrially are performed by many bacterial species that can oxidize ferrous iron and sulfur. An example of such species is Acidithiobacillus ferroxidans. Some fungi species (Aspergillus niger and Penicillium simplicissimum) have also been shown to have the ability to dissolute heavy metals. When fungi are used, the leaching mechanism is different. The fungi use the acids that they produce in their metabolic reactions to dissolve the metal.
In general, bioleaching is cleaner and safer for the environment than chemical processing. However environmental pollution with toxic products, like sulfuric acid from the pyrite leaching, and heavy metals is still possible. Another drawback of microbial leaching is the slow rate at which microbes work. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.06%3A_Microbial_Bioremediation/16.6A%3A_Microbial_Ore_Leaching.txt |
Petroleum oil can be degraded by microorganisms that use it as a source of energy.
Learning Objectives
• Show how microbes biodegrade petroleum waste
Key Points
• Biodegradation is the process of breaking down material in simpler components by living organisms, most often microorganisms.
• Oil spills occur due to accidents in the industry as a result of extraction or transportation. Since such spills spread over great areas and have deleterious effects on living organisms. It is important to use environmentally friendly mechanisms for their cleanup.
• There are many microorganisms that can break down petroleum, the most prominent being hydrocarbonoclastic bacteria. A representative of this group is Alcanivorax borkumensis, and its genome contains genes that code for the degradation of alkanes.
Key Terms
• hydrocarbons: Organic compounds made only of carbon and hydrogen. Examples include alkanes, alkenes, and aromatic hydrocarbons.
• emulsification: The process of forming a mixture of substances that are nonmixable under normal conditions.
• tarball: A blob of petroleum oil.
Biodegradation is the process in which living organisms, most often microorganisms, break down material into simpler components. Such material is usually organic matter that could be dissolved into chemical elements by organisms that possess the metabolic pathways to perform the reactions. Some microorganisms produce enzymes that can degrade a variety of chemical compounds, including hydrocarbons like oil.
Petroleum (crude oil) is a liquid fossil fuel. It is a product of decaying organic matter, such as algae and zooplankton. It is one of the major energy sources in the world, and is also used by the chemical industry to manufacture a large number of consumer products. However, oil drilling or transportation can cause accidents that lead to contamination of the environment. Oil spills in marine environments are especially damaging because they cannot be contained and can spread over huge areas. The aromatic compounds in oil are toxic to living organisms and such spills can render havoc in an ecosystem. Natural seepages from unexplored oil sources is another source of contamination.
In the environment, such spills are naturally cleaned by microorganisms that can break down the oil. The dominant group of such bacteria are the hydrocarbonoclastic bacteria (HCB). The concentration of these bacteria increases significantly in areas of oil spill. One of the best studied representative of this group is Alcanivorax borkumensis; it’s also the only one to have its genome sequenced. This species contains individual genes responsible for breaking down certain alkanes into harmless products. It also possesses genes to direct the production of a layer of biosurfactant around the cell to enhance the oil emulsification. The addition of nitrogen and phosphorus to the Alcanivorax environment increases its growth rate. However, the addition of these nutrients in natural environments to improve the cleanup of oil spills is not desirable, since it can have an overall negative impact on the ecosystem.
Aside from hydrocarbons, crude oil contains additional toxic compounds, such as pyridine. These are degraded by representatives of other genera such as Micrococcus and Rhodococcus. Oil tarballs are biodegraded slowly by species from the genera Chromobacterium, Micrococcus, Bacillus, Pseudomonas, Candida, Saccharomyces and others. In the clean up of the Deepwater Horizon oil spill, genetically modified microorganisms were used, but some scientists suspect they might have caused health issues for people in the affected areas. | textbooks/bio/Microbiology/Microbiology_(Boundless)/16%3A_Microbial_Ecology/16.06%3A_Microbial_Bioremediation/16.6B%3A_Petroleum_Biodegradation.txt |
Microorganisms are crucial participants in the detoxification of water and soil.
Learning Objectives
• Distinguish bioremediation of soil vs. water
Key Points
• Bacteria decompose organic matter by producing a number of different enzymes for more general reactions such as hydrolysis, acetogenesis and methanogenesis, and highly specific enzymes such as deoxygenases that can break aromatic compounds.
• Bacterial species are assisted in the process of degradation by fungi (e.g., Aspergillus sp.), protozoa, and representatives of Archaea.
• The recent advances in genomics, proteomics, and bioinformatics fields allow new insights into the tremendous metabolic potential of microorganisms.
Key Terms
• bioremediation: The use of biological organisms, usually microorganisms, to remove contaminants, especially from polluted water.
• bioavailability: The amount of matter that is physicochemically accesible for degradation by microorganisms.
Our planet is contaminated with many chemicals that are toxic to living organisms. These chemicals are products or byproducts from different industries. Examples of such contaminants are polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), chloroethenes, and pharmaceutical substances. These pollutants can cause dangerous contamination of the air, soil, and water. Microorganisms play a major role in eliminating such pollutants from the environment.
Bioremediation of Soil
Soil is a major reservoir of microorganisms with each gram containing about one billion microbes. Microbes are used for bioremediation in situ of contaminated soil. Microorganisms that can remove contaminants from the environment are called bioremediators. Contaminations are most often caused by a mixture of pollutants and the best strategy for cleanup is to use a cocktail of different species since each one of them will be optimized for the degradation of a specific toxic compound.
The microbe activity is usually monitored on such sites to ensure optimal conditions for bacterial growth and hence degradation. Decomposition of the toxic substances can be performed both in the presence (aerobically) and absence (anaerobically) of oxygen. The limiting factor for bioremediaton in soils is the bioavailability of the contaminant agents.
Bioremediation of Water
The treatment of sewage water is a critical process to assure the purification of wastewater that will prevent chemical and microbiological pollution of the environment, especially for the drinking water supplies. An important part of this process is the biological step which involves the activity of living organisms to clean the water from organic matter. This happens in the secondary step of sewage purification. Microorganisms substantially lessen the concentration of nutrients which if released in the environment can lead to undesirable overgrowth of microorganisms and algae.
They also have the potential to clean the water from toxic components. The degradation is performed in the anaerobic, aerobic, and composting steps. Anaerobic digestion by bacteria is allowed to procede for almost two weeks to guarantee enough time to complete the process. During this time, the organic matter undergoes four different enzymatic transformations: hydrolysis, acidogenesis, acetogenesis and methanogenesis. The final products are water, carbon dioxide, and methane. In the aerobic step, oxygen is added into the system and the organic matter is converted to carbon dioxide. In the composting step, additional carbon sources are added to aid the final steps of degradation.
In recent years, advances in genomics, proteomics, and bioinformatics studies of environmental microorganisms have revealed a tremendous potential in metabolic pathways.
Such studies showed that Burkholderia xenovorans LB400 and Rhodococcus sp. strain RHA1, have evolved pathways to degrade aromatic compounds, which are some of the toughest contaminants to eliminate. The bacteria have genes coding for deoxygenases to open the aromatic ring structures of these chemicals.
Hydrocarbons and their derivatives were long believed to be degraded only in the presence of oxygen. This would often lead to oxygen depletion in environments heavily polluted with oil. Studies in recent years have proven that there are numerous anaerobic bacterial species capable of decomposing this group of pollutants. A common feature among these bacteria is that they possess reductive dehalogenases.
Bacterial species are assisted in the process of degradation by fungi (e.g., Aspergillus sp.), protozoa, and representatives of Archaea. The primary role of fungi is in secreting numerous extracellular enzymes that break down complex molecules into their components and make them readily available to the bacterial community.
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Industrial microbiology is a branch of biotechnology that applies microbial sciences to create industrial products in mass quantities. There are multiple ways to manipulate a microorganism to increase maximum product yields. Introduction of mutations into an organism many be accomplished by introducing them to mutagens. The medical application to industrial microbiology is the production of new drugs synthesized in a specific organism for medical purposes
Thumbnail: Märzen at Oktoberfest, served in the traditional 1-liter Maß.
17: Industrial Microbiology
There are various types of microorganisms that are used for large-scale production of industrial items.
Learning Objectives
• Describe how microorganisms are used in industry to manufacture food or products in large quantities
Key Points
• The ability of specific microorganisms to produce specialized enzymes and proteins has been exploited for many purposes in industry.
• Industrial microorganisms are used to produce many things, including food, cosmetics, pharmaceuticals and construction materials.
• Microorganisms can be genetically modified or engineered to aid in large-scale production.
Key Terms
• exopolysaccharide: a type of sugar-composed polymer secreted by a microorganism into the external environment
• archaea: a taxonomic domain of single-celled organisms lacking nuclei that are fundamentally from bacteria.
Industrial microbiology includes the use of microorganisms to manufacture food or industrial products in large quantities. Numerous microorganisms are used within industrial microbiology; these include naturally occurring organisms, laboratory selected mutants, or even genetically modified organisms (GMOs). Currently, the debate in the use of genetically modified organisms (GMOs) in food sources is gaining both momentum, with more and more supporters on both sides. However, the use of microorganisms at an industrial level is deeply rooted into today’s society. The following is a brief overview of the various microorganisms that have industrial uses, and of the roles they play.
Archaea are specific types of prokaryotic microbes that exhibit the ability to sustain populations in unusual and typically harsh environments. Those suriving in the most hostile and extreme settings are known as extremophile archaea. The isolation and identification of various types of Archaea, particularly the extremophile archaea, have allowed for analysis of their metabolic processes, which have then been manipulated and utilized for industrial purposes.
Extremophile archaea species are of particular interest due to the enzymes and molecules they produce that allow them to sustain life in extreme climates, including very high or low temperatures, extremely acid or base solutions, or when exposed to other harmful factors, including radiation. Specific enzymes which have been isolated and used for industrial purposes include thermostable DNA polymerases from the Pyrococcus furiosus. This type of polymerase isa common tool in molecular biology; it is capable of withstanding the high temperatures that are necessary to complete polymerase chain reactions. Additional enzymes isolated from Pyrococcus speciesinclude specific types of amylases and galactosidases which allow food processing to occur at high temperatrues as well.
Corynebacteria are characterized by their diverse origins. They are found in numerous ecological niches and are most often used in industry for the mass production of amino acids and nutritional factors. In particular, the amino acids produced by Corynebacterium glutamicum include the amino acid glutamic acid. Glutamic acid is used as a common additive in food production, where it is known as monosodium glutamate (MSG). Corynebacterium can also be used in steroid conversion and in the degradation of hydrocarbons. Steroid conversion is an important process in the development of pharmaceuticals. Degradation of hydrocarbons is key in the breakdown and elimination of environmental toxins. Items such as plastics and oils are hydrocarbons; the use of microorganisms which exhibit the ability to breakdown these compounds is critical for environmental protection.
Xanthomonas, a type of Proteobacteria, is known for its ability to cause disease in plants. The bacterial species which are classified under Xanthomonasexhibit the ability to produce the acidic exopolysaccharide commonly marketed as xanthan gum, used as a thickening and stabilizing agent in foods and in cosmetic ingredients to prevent separation.
Another type of microorganism utilized by industry includes various species of Aspergillus. Thisgenusincludes several hundred types of mold. Aspergillus has become a key component in industrial microbiology, where it is used in the production of alcoholic beverages and pharmaceutical development. Aspergillus niger is most commonly used to produce citric acid, which is used in numerous products ranging from household cleaners, pharmaceuticals, foods, cosmetics, photography and construction. Aspergillus is also commonly used in large-scale fermentation in the production of alcoholic beverages such as Japanese sake. | textbooks/bio/Microbiology/Microbiology_(Boundless)/17%3A_Industrial_Microbiology/17.01%3A_Industrial_Microbiology/17.1A%3A_Industrial_Microorganisms.txt |
Learning Objectives
• Describe how Taq polymerase, restriction enzymes and DNA ligase are used in molecular biology
The expansion and growing popularity of the field of molecular biology has resulted in a higher demand for tools used to study molecular biology. The field of molecular biology specifically deals with the molecular mechanisms of a cell and focuses on the regulation of cellular interactions. Topics of particular interest within the field include gene expression (transcription and translation) and protein synthesis. Studying these mechanisms in the laboratory has been made possible by the use of molecules derived from microbes. The following is a brief overview of some of the molecular products derived from microbes that allow for the performance of popular molecular biology techniques.
Taq Polymerase
Taq polymerase is an enzyme that was first isolated from the microbe Thermus aquaticus. T. aquaticus is a specific type of bacterial species, a DNA polymerase, that is thermostable — it can withstand extremely high temperatures. The isolation of this polymerase has resulted in the ability to perform polymerase chain reactions (PCR), a process used to amplify DNA segments, in a single step. Prior to the isolation of Taq polymerase, a new DNA polymerase had to be added to the reaction after every cycle because of thermal denaturation. With the addition of Taq polymerase to the reaction tube, the cycle can be performed much more quickly, and less enzyme needs to be used. Currently, Taq polymerase is manufactured and produced on a large scale and is available for commercial sale.
Restriction Enzymes
Restriction enzymes are a specific class of enzymes isolated from various bacteria and archaea, in which they grow naturally as a means of protection against viral infection. These enzymes have the ability to cut DNA at specific recognition sequences and have served as invaluable tools in DNA modification and manipulation. The enzymes have the ability to recognize foreign DNA and cut it up. The bacteria and archaea from which these enzymes are isolated from have innate mechanisms to protect their own DNA sequences from these enzymes, such as methylation. The isolation of approximately 3000 restriction enzymes has allowed molecular biologists to utilize them in processes such as cloning and the production of recombinant DNA.
DNA Ligase
Another enzyme that was isolated from T. aquaticus and that has been undeniably important to the field of molecular biology is DNA ligase. DNA ligase plays a key role in molecular biology processes due to its ability to insert DNA fragments into plasmids. The process of DNA ligation is defined as the ability of DNA ligase to covalently link, or ligate, fragments of DNA together. In molecular biology — specifically, during the process of developing recombinant DNA — DNA ligase can be used to ligate a fragment of DNA into a plasmid vector. The most commonly used DNA ligase is derived from the T4 bacteriophage and is referred to as T4 DNA ligase.
Key Points
• Various enzymes can be isolated from microorganisms and utilized in recombinant – DNA production.
• The ability of some archaea to thrive in extreme environments has led to analysis and isolation of important molecular components of the organisms, such as Taq polymerase, that have contributed to modern molecular biology techniques.
• Modern-day molecular biology techniques rely heavily on specific enzymes and molecular components derived from microbes, including DNA ligase and restriction enzymes.
• DNA ligase functions by covalently linking, or ligating, DNA fragments.
• Restriction enzymes function by recognizing and cutting specific sequences within DNA.
Key Terms
• polymerase chain reaction: A technique in molecular biology for creating multiple copies of DNA from a sample; used in genetic fingerprinting etc.
• restriction enzymes: an endonuclease that cuts DNA at specific recognition sequences | textbooks/bio/Microbiology/Microbiology_(Boundless)/17%3A_Industrial_Microbiology/17.01%3A_Industrial_Microbiology/17.1B%3A_Molecular_Products_from_Microbes.txt |
Primary and secondary metabolites are often used in industrial microbiology for the production of food, amino acids, and antibiotics.
Learning Objectives
• Describe how primary and secondary metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals for organic synthesis
Key Points
• Primary metabolites are considered essential to microorganisms for proper growth.
• Secondary metabolites do not play a role in growth, development, and reproduction, and are formed during the end or near the stationary phase of growth.
• These metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals necessary for organic synthesis.
Key Terms
• bradycardia: the slowing of the heartbeat to below average
Bacterial metabolism can be classified into three major categories: the kind of energy used for growth, the carbon source, and the electron donors used for growth. Pathogenic bacteria are capable of exhibiting various types of metabolism. Metabolites, the intermediates and products of metabolism, are typically characterized by small molecules with various functions. Metabolites can be categorized into both primary and secondary metabolites. These metabolites can be used in industrial microbiology to obtain amino acids, develop vaccines and antibiotics, and isolate chemicals necessary for organic synthesis.
Primary Metabolites
Primary metabolites are involved in growth, development, and reproduction of the organism. The primary metabolite is typically a key component in maintaining normal physiological processes; thus, it is often referred to as a central metabolite. Primary metabolites are typically formed during the growth phase as a result of energy metabolism, and are deemed essential for proper growth. Examples of primary metabolites include alcohols such as ethanol, lactic acid, and certain amino acids. Within the field of industrial microbiology, alcohol is one of the most common primary metabolites used for large-scale production. Specifically, alcohol is used for processes involving fermentation which produce products like beer and wine. Additionally, primary metabolites such as amino acids– including L-glutamate and L-lysine, which are commonly used as supplements– are isolated via the mass production of a specific bacterial species, Corynebacteria glutamicum. Another example of a primary metabolite commonly used in industrial microbiology includes citric acid. Citric acid, produced by Aspergillus niger, is one of the most widely used ingredients in food production. It is commonly used in pharmaceutical and cosmetic industries as well.
Secondary Metabolites
Secondary metabolites are typically organic compounds produced through the modification of primary metabolite synthases. Secondary metabolites do not play a role in growth, development, and reproduction like primary metabolites do, and are typically formed during the end or near the stationary phase of growth. Many of the identified secondary metabolites have a role in ecological function, including defense mechanism(s), by serving as antibiotics and by producing pigments. Examples of secondary metabolites with importance in industrial microbiology include atropine and antibiotics such as erythromycin and bacitracin. Atropine, derived from various plants, is a secondary metabolite with important use in the clinic. Atropine is a competitive antagonist for acetycholine receptors, specifically those of the muscarinic type, which can be used in the treatment of bradycardia. Antibiotics such as erythromcyin and bacitracin are also considered to be secondary metabolites. Erythromycin, derived from Saccharopolyspora erythraea, is a commonly used antibiotic with a wide antimicrobial spectrum. It is mass produced and commonly administered orally. Lastly, another example of an antibiotic which is classified as a secondary metabolite is bacitracin. Bacitracin, derived from organisms classified under Bacillus subtilis, is an antibiotic commonly used a topical drug. Bacitracin is synthesized in nature as a nonribosomal peptide synthetase that can synthesize peptides; however, it is used in the clinic as an antibiotic. | textbooks/bio/Microbiology/Microbiology_(Boundless)/17%3A_Industrial_Microbiology/17.01%3A_Industrial_Microbiology/17.1C%3A_Primary_and_Secondary_Metabolites.txt |
Large-scale fermentations are key to the production of numerous products ranging from food to pharmaceutical items.
Learning Objectives
• Describe fermentation and its applications to produce food, alcoholic beverages, fuel and recombinant products such as insulin
Key Points
• Large-scale fermentations are utilized to create massive quantities of ethanol which are used for food production, alcohol production, and even gasoline production.
• Fermentation is characterized by the metabolic processes that are used to transfer electrons released from nutrients to molecules obtained from the breakdown of those same nutrients.
• Fermentation utilizes numerous organic compounds, such as sugars, as endogenous electron acceptors to promote the electron transfer that occurs.
Key Terms
• oxidation: A reaction in which the atoms of an element lose electrons and the valence of the element increases.
• amylase: A type of digestive enzyme capable of breaking down complex carbohydrates into simple sugars.
Fermentation includes the processes by which energy is extracted from the oxidation of organic compounds. The oxidation of organic compounds occurs by utilizing an endogenous electron acceptor to transfer electrons released from nutrients to molecules obtained from the breakdown of these same nutrients.
There are various types of fermentation which occur at the industrial level such as ethanol fermentation and fermentation processes used to produce food and wine. The ability to utilize the fermentation process in anaerobic conditions is critical to organisms which demand ATP production by glycolysis. Fermentation can be carried out in aerobic conditions as well, as in the case of yeast cells which prefer fermentation to oxidative phosphorylation. The following is a brief overview of a few types of the large-scale fermentations utilized by industries in production creation.
Ethanol Fermentation
Ethanol fermentation is used to produce ethanol for use in food, alcoholic beverages, and both fuel and industry. The process of ethanol fermentation occurs when sugars are converted into cellular energy. The sugars which are most often used include glucose, fructose, and sucrose. These sugars are converted into cellular energy and produce both ethanol and carbon dioxide as waste products. Yeast is the most commonly used organism to produce ethanol via the fermentation process for beer, wine, and alcoholic drink production. As stated previously, despite abundant amounts of oxygen which may be present, yeast prefer to utilize fermentation. Hence, the use of yeast on a large-scale to produce ethanol and carbon dioxide occurs in an anaerobic environment.
The ethanol which is produced can then be used in bread production. Yeast will convert the sugars present in the dough to cellular energy and produce both ethanol and carbon dioxide in the process. The ethanol will evaporate and the carbon dioxide will expand the dough. In regards to alcohol production, yeast will induce fermentation and produce ethanol. Specifically, in wine-making, the yeast will convert the sugars present in the grapes. In beer and additional alcohol such as vodka or whiskey, the yeast will convert the sugars produced as a result of the conversion of grain starches to sugar by amylase. Additionally, yeast fermentation is utilized to mass produce ethanol which is added to gasoline. The major source of sugar utilized for ethanol production in the US is currently corn; however, crops such as sugarcane or sugar beets can be used as well.
Recombinant Products
Fermentation is also utilized in the mass production of various recombinant products. These recombinant products include numerous pharmaceuticals such as insulin and hepatitis B vaccine. Insulin, produced by the pancreas, serves as a central regulator of carbohydrate and fat metabolism and is responsible for the regulation of glucose levels in the blood. Insulin is used medically to treat individuals diagnosed with diabetes mellitus. Specifically, individuals with type 1 diabetes are unable to produce insulin and those with type 2 diabetes often develop insulin resistance where the hormone is no longer effective.
The increase in individuals diagnosed with diabetes mellitus has resulted in an increase in demand for external insulin. The mass production of insulin is performed by utilizing both recombinant DNA technology and fermentation processes. E. coli, which has been genetically altered to produce proinsulin, is grown to a large amount to produce sufficient amounts in a fermentation broth. The proinsulin is then isolated via disruption of the cell and purified. There is further enzymatic reactions that occur to then convert the proinsulin to crude insulin which can be further altered for use as a medicinal compound.
An additional recombinant product that utilizes the fermentation process to be produced is the hepatitis B vaccine. The hepatitis B vaccine is developed to specifically target the hepatitis B virus infection. The creation of this vaccine utilizes both recombinant DNA technology and fermentation. A gene, HBV, which is specific for hepatitis B virus, is inserted into the genome of the organism yeast. The yeast is used to grow the HBV gene in large amounts and then harvested and purified. The process of fermentation is utilized to grow the yeast, thus promoting the production of large amounts of the HBV protein which was genetically added to the genome.
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• Archaea. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Archaea%23Significance_in_technology_and_industry. License: CC BY-SA: Attribution-ShareAlike
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• amylase. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/amylase. License: CC BY-SA: Attribution-ShareAlike
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• Fermentation (biochemistry). Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ferment...(biochemistry). License: Public Domain: No Known Copyright
• Ethanol fermentation. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Ethanol_fermentation. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/17%3A_Industrial_Microbiology/17.01%3A_Industrial_Microbiology/17.1D%3A_Large-Scale_Fermentations.txt |
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