FINAL Micro topics + Pract Flashcards

Question

Trichinella spiralis

Answer 1

Trichinella spiralis causes trichinosis * The life cycle of T. spiralisinvolves mammal reservoirs (pigs most importantly) and humans as end-stage hosts - Humans are infected by eating raw or undercooked meat containing larvae encysted in the muscle - The larvae excyst and mature into adults within the mucosa of the small intestine - Eggs hatch within the adult females, and larvae are released and distributed via the bloodstream to many organs; however, they develop in striated muscle cells - Within these “nurse cells“, they encyst within a fibrous capsule and can remain viable for several years but eventually calcify * Diarrhea usually develops after eating undercooked meat (usually pork), followed 1 to 2 weeks later by fever, muscle pain, periorbital edema, subconjunctival hemorrhages (important diagnostic criterion), and eosinophilia * Signs of cardiac and CNS disease are frequent, because the larvae migrate to these tissues as well * Death, which is rare, is usually due to congestive heart failure or respiratory paralysis * Trichinosis occurs worldwide, especially in Eastern Europe and West Africa * Muscle biopsy reveals larvae within striated muscle, and serologic tests become positive 3 weeks after infection * There is no effective treatment for trichinosis when the larvae have infected the muscle, but for patients with severe symptoms, steroids plus albendazole can be useful

Answer 2

Cestodes Diphyllobothrium latum * Diphyllobothrium latum (fish tapeworm) causes diphyllobothriasis * Humans are infected by ingesting raw or undercooked fish containing plerocercoid larvae (a.k.a. spraganum larvae) - In the small intestine, the larvae attach to the gut wall and develop into adult worms - Gravid proglottids release fertilized eggs through a genital pore, and the eggs are then passed in the stools (must go into fresh water for life cycle to continue) - The embryos emerge from the eggs and are eaten by tiny copepod crustacea (first intermediate host) - There the embryos differentiate and form procercoid larvae in the body cavity - When the copepod is eaten by freshwater fish (e.g. pike, trout, perch), the larvae differentiate into plerocercoids in the muscle of the fish (second intermediate host) - The cycle is complete when raw or undercooked fish is eaten by humans (definitive host) * Infection by D. latum causes little damage in the small intestine and therefore most patients are asymptomatic, but abdominal discomfort and diarrhea can occur * Megaloblastic anemia occurs in some individuals as a result of vitamin B12 deficiency caused by the preferential uptake of the vitamin by the worm * The disease is found worldwide but is endemic in areas where eating raw fish is custom (Scandinavia, northern Russia, Japan, etc.) * Diagnosis depends on finding the typical eggs (i.e. oval, yellow-brown eggs with an operculum at one end) in the stools * The treatment of choice is praziquantel Hymenolepis nana * Hymenolepis nana (dwarf tapeworm) is the most frequently found tapeworm in the US * It is different from other tapeworms because its eggs are directly infectious for humans (i.e. ingested eggs can develop into adult worms without an intermediate host) - Within the duodenum, the eggs hatch and differentiate into cysticercoid larvae and then into adult worms - Gravid proglottids detach, disintegrate, and release fertilized eggs - The eggs either pass in the stool or can reinfect the small intestine (autoinfection) - A possible intermediate host for H. nana are is arthropods, which can ingest the eggs passed in human stool * Infection causes little damage, and most patients are asymptomatic * The organism is found worldwide, commonly in the tropics * Diagnosis is based on finding eggs in stools (characteristically have 8-10 polar filaments between the membrane of the six-hooked larva and the outer shell) * The treatment of choice is praziquantel

Answer 3

There are two important human pathogens in the genus Taenia: T. solium (pork tapeworm) and T. saginata (beef tapeworm). Taenia solium * The adult form of T. solium causes taeniasis, whereas the larvae of T. solium cause cysticercosis * Humans are infected by eating raw or undercooked pork containing the cysticercoid larvae In the small intestine, the larvae attach to the gut wall and take about 3 months to grow into adult worms measuring up to 5 m - The gravid terminal proglottids containing many eggs detach daily, are passed in the feces, and are accidentally eaten by pigs (intermediate host) - A six-hooked embryo (oncosphere) emerges from each egg in the pig‘s intestine - The embryos burrow into a blood vessel and are carried to skeletal muscle, where they develop into cysticerci and remain until eaten by a human (definitive host) * In cysticercosis, a more dangerous sequence occurs when a person ingests the worm eggs in food or water that has been contaminated with human feces - The eggs hatch in the small intestine, and the oncospheres burrow through the wall into a blood vessel - They can disseminate to many organs, especially the eyes and brain, where they encyst to form cysticerci * The adult tapeworm attached to the intestinal wall causes little damage and most patients infected by them are asymptomatic, but anorexia and diarrhea can occur * The cysticerci, on the other hand, can become very large, especially in the brain, where they manifest as a space-occupying lesion - Living cysticerci do not cause inflammation, but when they die they release substances that provoke an inflammatory response - Eventually the cysticerci calcify - Cysticercosis in the brain causes headaches, vomiting, and seizures - Cysticercosis in the eyes can appear as uveitis or retinitis * The disease occurs worldwide but is endemic in areas of Asia, South America, and Eastern Europe * Identification of T. solium consists of finding gravid proglottids with 5-10 primary uterine branches in the stools * Diagnosis of cysticercosis depends on demonstrating the presence of cyst in tissue * The treatment of choice is praziquantel Taenia saginata * Taenia saginata causes taeniasis * T. saginata larvae do not cause cysticercosis * The life cycle of T. saginata follows the same steps as the life cycle of T. solium, with the exception that consumption of raw or undercooked beef is the cause of infection and cattle are the intermediate host * Little damage results from the presence of adult worm in the small intestine and most patients infected by them are asymptomatic, but malaise and mild cramps can occur * The disease occurs worldwide but is endemic in Africa, South America, and Eastern Europe The proglottids are motile and may cause pruritus ani as they move on the skin adjacent to the anus * Identification of T. saginata consists of finding gravid proglottids with 15-20 uterine branches in the stool * The treatment of choice is praziquantel

Answer 4

Echinococcus * Echinococcus granulosus (dog tapeworm) causes echinococcosis * The larvae of E. granulosus cause unilocular hydatid cyst disease * In the typical life cycle, adult worms in the dog‘s (definitive host) intestine liberate thousands of eggs, which are ingested by sheep (intermediate host) and humans (dead-end intermediate host) - The oncosphere embryos emerge in the small intestine and migrate primarily to the liver but also to the lungs, bones, and brain - The embryos develop into large fluid-filled hydatid cysts, containing many protoscoleces - The life cycle is completed when the entrails (e.g. liver containing hydatid cysts) of slaughtered sheep are eaten by dogs * The cyst formed by E. granulosus acts as a space-occupying lesion, putting pressure on adjacent tissue - Many individuals are asymptomatic, but liver cysts may cause hepatic dysfunction - Cysts in the lungs can erode into a bronchus, causing bloody sputum - Cerebral cysts can cause headache and focal neurologic signs - If the cyst ruptures spontaneously or during trauma or surgical removal, life-threatening anaphylactic shock can occur * The disease is found primarily in shepherds living in the Mediterranean region, the Middle East, and Australia * Treatment involves albendazole with or without surgical removal of the cyst * Echinococcus multilocularis shows many of the same features as those of E. granulosus, but the definitive hosts are mainly foxes and the intermediate hosts are various rodents - Within the human liver, the larvae form multiloculated cysts with few protoscoleces - The clinical picture usually involves jaundice and weight loss and the prognosis is poor Dipylidium caninum * Dipylidium caninum is the most common tapeworm of dogs and cats * It occasionally infects human, usually young children, when dog or cat fleas carrying cysticerci are ingested - The cysticerci develop into adult tapeworms in the small intestine * Most human infections are asymptomatic, but diarrhea and pruritus ani can occur * Diagnosis is made by observing the typical “barrel-shaped“ proglottids in the stool or diapers * Niclosamide is the drug of choice

Answer 5

Trematodes Schistosoma * Schistosoma (blood fluke) causes schistosomiasis * Schistosoma mansoni and Schistosoma japonicum affect the gastrointestinal tract, whereas Schistosoma haematobium affects the urinary tract In contrast to other trematodes, which are hermaphrodites, adult schistosomes exist as separate sexes but live attached to each other * Humans are infected when the free-swimming, fork-tailed cercariae penetrate the skin - They differentiate to schistosomula larvae, enter the blood, and are carried via the veins into the arterial circulation - Those that enter the sup. mesenteric artery pass into the portal circulation and reach the liver, where they mature into adult flukes - In the definitive venous site (mesenteric venules for S. mansoni and S. japonicum, bladder veins for S. haematobium) the female lays fertilized eggs, which penetrate the vascular endothelium and enter the gut or bladder lumen, respectively - The eggs are excreted in the stools or urine and must enter fresh water where they release ciliated, swimming larvae called miracidia - The miracidia then penetrate snails (intermediate host) and undergo further development and multiplication to produce many cercariae - Cercariae leave the snails, enter fresh water, and complete the cycle by penetrating human skin * Most of the pathologic findings are caused by the presence of eggs in the liver, spleen, or wall of the gut or bladder - Eggs in the liver induce granulomas, which lead to fibrosis, hepatomegaly, and portal hypertension that leads to splenomegaly - S. mansoni eggs damage the wall of the distal colon, whereas S. japonicum eggs damage the walls of the small and large intestine, leading to infection and GI hemorrhage - The eggs of S. haematobium in the wall of the bladder induce granuloma and fibrosis, which can lead to carcinoma of the bladder * Most patients are asymptomatic, but chronic infections may become symptomatic * The acute stage, which begins shortly after cercarial penetration, consists of itching and dermatitis followed 2 to 3 weeks later by fever, chills, diarrhea, lymphadenopathy, and hepatosplenomegaly * “Swimmer‘s itch“, which consists of pruritic papules, is a frequent problem in many lakes in the US and occurs due to an immunologic reaction to the presence in the skin of the cercariae of non-human schistosomes * S. mansoni is found in Africa and Latin America, S. haematobium is found in Africa and the Middle East, and S. japonicum is found only in Asia * The three species can be distinguished by the appearance of their eggs in the microscope - S. mansoni: prominent lateral spine - S. japonicum: very small lateral spine - S. haematobium: terminal spine * The treatment of choice is praziquantel Paragonimus * Paragonimus westermani (lung fluke) causes paragonimiasis * Humans are infected by eating raw or undercooked crab meat (or crayfish) containing the encysted metacercariae larvae - After excystation in the small intestine, immature flukes penetrate the intestinal wall and migrate through the diaphragm into the lung parenchyma - There, they differentiate into hermaphroditic adults and produce eggs that enter the bronchioles and are coughed up or swallowed - Eggs in either sputum or feces that reach fresh water hatch into miracidia, which enter snails (first intermediate hosts) - There, they differentiate first into rediae larvae and then into many free-swimming cercariae - The cercariae infect and encyst in freshwater crabs (second intermediate host) and the cycle is complete when undercooked infected crabs are eaten by humans * The main symptom is a chronic cough with bloody sputum, accompanied by dyspnea, pleuritic chest pain, and recurrent attacks of bacterial pneumonia - The disease can resemble tuberculosis * Paragonimiasis is endemic in Asia and India * The treatment of choice is praziquantel Clonorchis * Clonorchis sinensis causes clonorchiasis (Asian liver fluke infection) * Humans are infected by eating raw or undercooked fish containing the encysted metacercariae larvae - After excystation in the duodenum, immature flukes enter the biliary ducts and differentiate into adults - The hermaphroditic adults produce eggs, which are excreted in the feces - Upon reaching fresh water, the eggs are ingested by snails (first intermediate host) - The eggs hatch within the gut and differentiate first into rediae larvae and then into many free-swimming cercariae - Cercariae encyst under the scales of certain freshwater fish (second intermediate host), which are then eaten by humans * Most infections are asymptomatic, but upper abdominal pain, anorexia, hepatomegaly, and eosinophilia can occur in patients with a heavy worm burden * In some infections, the inflammatory response can cause hyperplasia and fibrosis of the biliary tract, but often there are no lesions * Chlonorchiasis is endemic in China, Japan, Korea, and Indochina * The treatment of choice is praziquantel Fasciola * Fasciola hepatica (sheep liver fluke) causes disease primarily in sheep and other domestic animals in Latin America, Africa, Europe, and China * Humans are infected by eating watercress (or other aquatic plants) contaminated by metacercariae larvae that excyst in the duodenum, penetrate the gut wall, and reach the liver, where they mature into adults - Hermaphroditic adults in the bile ducts produce eggs, which are excreted in the feces - The eggs hatch in fresh water, and miracidia enter the snails - Miracidia develop into cercariae, which then encyst on aquatic vegetation - Sheep and humans eat the plants, thus completing the life cycle * Symptoms are primarily due to the presence of adult worm in the biliary tract - In early infection, right-upper-quadrant pain, fever, and hepatomegaly can occur, but most infections are asymptomatic - Months or years later, obstructive jaundice can occur - Halzoun is a painful pharyngitis caused by the presence of adult flukes on the posterior pharyngeal wall, acquired by eating raw sheep liver * Diagnosis is made by identification of eggs in the feces * The drug of choice is triclabendazole

Answer 6

Tissue nematodes Wuchereria * Wuchereria bancrofti causes filariasis * Humans are infected when the female mosquito deposits infective larvae on the skin while biting - The larvae penetrate the skin, enter a lymph node, and, after 1 year, mature to adults that produce microfilariae - These circulate in the blood, chiefly at night, and are ingested by biting mosquitoes - Within the mosquito, the microfilariae produce infective larvae that are transferred with the next bite * Early infections are asymptomatic, but later, fever, lymphangitis, and cellulitis develop * Adult worms in the lymph nodes cause inflammation that eventually obstructs the lymphatic vessels, causing massive edema of the legs (elephantiasis) * Microfilariae in the lung elicit an immediate hypersensitivity reaction that causes tropical pulmonary eosinophilia, characterized by coughing and wheezing, especially at night * The disease occurs in the tropical areas of Africa, Asia, and Latin America * Diethylcarbamazine is effective only against microfilariae; no drug therapy for adult worms is available Loa * Loa loa causes loiasis * Humans are infected by the bite of the deer fly, which deposits infective larvae on the skin - The larvae enter the bite wound, wander in the body, and develop into adults - The females release microfilariae that enter the blood, particularly during the day - The microfilariae are taken up by the fly during a blood meal and differentiate into infective larvae, which continue the cycle when the fly bites the next person * There is no inflammatory response to microfilariae or adults, but a hypersensitivity reaction causes transient, localized, non-erythematous, subcutaneous edema * The most dramatic finding is an adult worm crawling across the conjunctiva of the eye, a harmless but disconcerting event * The disease is found only in tropical Central and West Africa * The drug of choice is diethylcarbamazine Onchocerca * Onchocerca volvulus causes onchocerciasis * Humans are infected when the female blackfly, deposits infective larvae while biting - The larvae enter the wound and migrate into the subcutaneous tissue, where they differentiate into adults (usually within dermal nodules) - The female produces microfilariae that are ingested when another blackfly bites - The microfilariae develop into infective larvae in the fly to complete the cycle * Inflammation occurs in subcutaneous tissue, and pruritic papules and nodules form in response to the adult worm proteins - Thickening, scaling, and dryness of the skin accompanied by severe itching are the manifestations of a dermatitis often called “lizard skin“ * Microfilariae migrate through subcutaneous tissue, ultimately concentrating in the eyes where they cause lesions that can lead to blindness (river blindness) * The disease is a major cause of blindness in Africa and Central America * Diagnosis is based on identifying microfilariae in biopsy of the affected skin * Ivermectin is effective against microfilariae but not adults, therefore suramin, which kills adult worms but is quite toxic, can be given in addition Dracunculus * Dracunculus medinensis (guinea fire worm) causes dracunculiasis * Humans are infected when tiny crustaceans containing infective larvae are swallowed in drinking water - The larvae are released in the small intestine and migrate into the body, where they develop into adults that cause the skin to ulcerate and then release motile larvae into fresh water - Crustaceans eat the larvae, which molt to form infective larvae * The adult female produces a substance that causes inflammation, blistering, and ulceration of the skin, usually of the lower extremities - The inflamed papule burns and itches, and the ulcer can become secondarily infected * Diagnosis is usually made clinically by finding the worm in the skin ulcer * Thiabendazole and metronidazole can be given, but ultimately treatment relies on slow extraction of the worm from the skin ulcer

Answer 7

* Pneumocystis jirovecii is classified as a yeast on the basis of molecular analysis, but it has many characteristics of a protozoan and is therefore medically thought of as one * P. jirovecii is an important cause of pneumonia in immunocompromised individuals * Transmission occurs by inhalation and infection is predominantly in the lungs, although the organism does not invade the lungs * The presence of cysts in the alveoli induces an inflammatory response consisting primarily of plasma cells, resulting in a frothy exudate that blocks oxygen exchange - The sudden onset of fever, non-productive cough, dyspnea, and tachypnea is typical of Pneumocystis pneumonia - Bilateral rales and ronchi are heard, and the chest X-ray shows a diffuse interstitial pneumonia with “ground glass“ infiltrates bilaterally * Extrapulmonary infections occur in the late stages of AIDS and affect primarily the liver, spleen, lymph nodes, and bone marrow * The mortality rate of untreated Pneumocystis pneumonia approaches 100% * P. jirovecii is distributed worldwide and it is estimated that 70% of people have been infected * Diagnosis is typically made by finding the cysts of Pneumocystis in bronchial lavage specimens * The drug of choice is TMP-SMX

Answer 8

Fungal cell structure * Fungi (yeasts and molds) and bacteria differ in several aspects due to the fact that fungi are eukaryotic organisms, whereas bacteria are prokaryotic * Two fungal cell structures are important medically: (1) The fungal cell wall consists primarily of chitin (not peptidoglycan as in bacteria), but also contains other polysaccharides, such as β-glucan (site of action of the anti-fungal drug caspofungin) (2) The fungal cell membrane contains ergosterol (except for P. jirovecii, which contains cholesterol), which is the site of action of the amphotericin B and azole drugs (fluconazole, ketoconazole) * There are two types of fungi: yeasts and molds - Yeasts grow as single cells that reproduce by asexual budding - Molds grow as long filaments (hyphae) and form a mat (mycelium) § Some hyphae form transverse walls (septate hyphae), whereas others do not (non-septate hyphae) * Several medically important fungi are thermally dimorphic, i.e. they form different structures at different temperatures - They exist as molds in the environment at ambient temperature and as yeasts (or other structures) in human tissues at body temperature * Some fungi reproduce sexually by mating and forming sexual spores (e.g. zygospores, ascospores, and basidiospores) - Fungi that do not form sexual spores are termed “imperfect“ (fungi imperfecti) * Most fungi of medical interest propagate asexually by forming conidia (asexual spores; e.g. arthrospores, chlamydospores, blastospores, and sporangiospores) from the sides or ends of specialized structures * Fungi do not have endotoxin in their cell walls and do not produce bacterial-type exotoxins * Certain factors, such as the ALS (agglutinin-like sequence) family and secreted phospholipases, aid in the colonization of fungi - Secreted phospholipases can be found e.g. in C. albicans, A. fumigatus, and C. neoformans - Other factors, such as hydrophobic-hydrophobic interaction and co-aggregation with aerobic and anaerobic bacteria, also aid in colonization * During infection, the phenotypic switch between blastoconidia and hyphae is a virulence trait of C. albicans Diagnostic procedures in fungal infections * There are four approaches to the laboratory diagnosis of fungal diseases 1) Direct microscopic examination of clinical specimen - Sputum, lung biopsy specimen, and skin scrapings can be used - Depends on finding characteristic asexual spores, hyphae, or yeasts in the light microscope - Specimen is either treated with 10% potassium hydroxide (KOH) to dissolve tissue material or stained with special fungal stains - F.x. spherules of C. immitis and the wide capsule of Cryptococcus neoformans seen in India ink preparations of spinal fluid 2) Culture of the organism - Fungi are frequently cultured on Sabouraud‘s agar, which facilitates the appearance of the slow-growing fungi by inhibiting the growth of bacteria in the specimen (due to low pH and added antibiotics) - The appearance of the mycelium and the nature of the asexual spores are frequently sufficient to identify the organism 3) DNA probe tests - Identify colonies growing in culture at an earlier stage of growth than can tests based on visual detection of the colonies, leading to a more rapid diagnosis - Available for Coccidioides, Histoplasma, Blastomyces, and Cryptococcus 4) Serologic tests - Tests for the presence of antibodies in the patient‘s serum or spinal fluid are useful in diagnosing systemic mycoses but less so in diagnosing other fungal infections - The complement fixation test is most frequently used in suspected cases of coccidioidomycosis, histoplasmosis, and blastomycosis - In cryptococcal meningitis, the presence of polysaccharide capsular antigens of C. neoformans in the spinal fluid can be detected by the latex agglutination test

Answer 9

Dermatophytoses * Dermatophytes are fungi that infect only superficial keratinized structures (skin, hair, nails) and cause dermatophytoses (tinea, ringworm) * The most important dermatophytes are classified in three genera: Trichophyton, Epidermophyton, and Microsporum Dermatophytes are spread from infected persons by direct contact, and Microsporum is also spread from animals such as dogs and cats * Typical ringworm lesions have an inflamed circular border containing papules and vesicles surrounding a clear area of relatively normal skin * The disease is usually named after the affected body part, such as tinea capitis for the head, tinea corporis for the body, tinea cruris for the groin, and tinea pedis for the foot * Tinea unguium, also called onychomycosis, is a disease of the nails (especially toe nails), where they become thickened, broken, and discolored * In some infected persons, hypersensitivity causes dermatophytid (“id“) reactions (e.g. vesicles on the fingers), which are a response to circulating fungal antigens and do not contain hyphae * Scrapings of skin or nail placed in KOH on a glass slide show septate hyphae under microscopy * Cultures on Sabouraud‘s agar at room temperature develop typical hyphae and conidia * Microsporum species can be detected by seeing fluorescence when the lesions are exposed to ultraviolet light from a Wood‘s lamp * Topical terbinafine is the first-line therapy for tinea infections, but oral treatment with griseofulvin or itraconazole can also be used * Onychomycosis can be treated with efinaconazole solution applied topically to the nails - Lecture slides say that first-line therapy for onychomycosis is terbinafine (oral +/- topical) and the second-line therapy should consist of azoles (oral +/- topical) Malassezia furfur : Pityriasis versicolor Tinea versicolor * Tinea versicolor (pityriasis versicolor) is a superficial skin infection of cosmetic importance only and is caused by Malassezia species * The lesions are usually noticed as hypopigmented areas, especially on tanned skin in the summer * There might be slight scaling or itching, but usually infection is asymptomatic * It occurs more frequently in hot, humid weather * The lesions contain both budding yeast cells and hyphae * Diagnosis is usually made by observing this mixture in KOH preparations of skin scrapings * The treatment of choice is topical miconazole, but fluconazole or itraconazole can be used to treat recurrences - Selenium sulfide lotion can also be used Tinea nigra * Tinea nigra is an infection of the keratinized layers of the skin and is caused by Cladosporium werneckii * It appears as a brownish spot, caused by the melanin-like pigment in the hyphae, with abnormal thickening of the cornified epidermis (hyperkeratosis) * It can also manifest with pruritus * C. werneckii is typically found in the soil in tropical climates and transmitted during injury * Diagnosis is made by microscopic examination with KOH and culture of the skin scrapings * The infection is treated with a topical keratolytic agent (e.g. salicylic acid) as well as topical antifungal agents (itraconazole, terbinafine)

Answer 10

Sporothrix schenckii Sporotrichosis * Sporothrix schenckii is a dimorphic fungus - The mold form lives on plants and the yeast form occurs in human tissue * When spores of the mold are introduced into the skin, typically by a thorn, it causes a local pustule or ulcer with nodules along the draining lymphatics The lesions are typically painless, and there is little systemic illness - Some patients may present with arthritis and tenosynovitis * In HIV-infected patients with low CD4 counts, disseminated sporotrichosis can occur * Round or cigar-shaped budding yeasts are seen in tissue specimens * The drug of choice for skin lesions is itraconazole Chromomycosis * Chromomycosis is a slowly progressive granulomatous infection that is caused by several soil fungi (most often due to Fonsecaea pedroso, but also by Phialophora verrucosa and Cladosporium spp.) when introduced into the skin through trauma * Wart-like lesions with crusting abscesses extend along the lymphatics - After many years, the lesions may resemble the head of a cauliflower - Bacterial superinfection can lead to lymphedema and elephantiasis, and occasionally to squamous cell carcinoma at affected sites * The disease occurs mainly in the tropic and is found on bare feet and legs * In the clinical laboratory, dark brown, round fungal cells are seen in leukocytes or giant cells * The disease is treated with cryosurgery and itraconazole

Answer 11

Coccidioides immitis Coccidioides • Coccidioides immitis causes coccidioidomycosis • C. immitis is a dimorphic fungus that exists as a mold in soil and as a spherule in tissue • The fungus is endemic in the southwestern US and Latin America • It forms hyphae with alternating arthrospores in soil, which can be inhaled and infect the lungs - In the lungs, arthrospores form thick-walled spherules that are large (30 mm in diameter) and filled with endospores - Upon rupture of the wall, endospores are released and differentiate to form new spherules - Dissemination from the lungs to other organs (primarily bones and CNS) occurs in people who have a defect in cell-mediated immunity • Most infections of the lung are asymptomatic, but some infected persons develop an influenza-like illness with fever and cough - ~50% show changes in the lungs on X-ray and 10% develop erythema nodosum • Disseminated disease most commonly produces meningitis, osteomyelitis and skin nodules (NB: erythema nodosum is not a sign of disseminated disease, and is actually an indicator of good prognosis) • Diagnosis can be done microscopically (shows spherules), with culture (shows hyphae with arthrospores), with serology, or with PCR No treatment is needed in asymptomatic or mild primary infection • Amphotericin B or itraconazole is used for persisting lung lesions or disseminated disease • Fluconazole is the drug of choice for meningitis and is also effective in lung disease Histoplasma capsulatum Histoplasma • Histoplasma capsulatum causes histoplasmosis • This fungus occurs in many parts of the world, and is endemic in central and eastern US states • H. capsulatum is a dimorphic fungus that exists as a mold in soil and as a yeast in tissue - It forms two types of asexual spores: (1) tuberculate macroconidia, which are important for laboratory identification; and (2) microconidia, which transmit the infection if inhaled • Inhaled spores are engulfed by macrophages and develop into yeast forms - The yeasts survive within the phagolysosome of the macrophage by producing alkaline substances, such as bicarbonate and ammonia, which inactivate the degradative enzymes of the phagolysosome - The organisms spread widely throughout the body, especially to the liver and spleen - Most infections remain asymptomatic, with small granulomatous foci healing by calcification - Intense exposure produces pneumonia and cavitary lung lesions that may manifest with clinical problems - Disseminated histoplasmosis develops in infants and individuals with reduced cellmediated immunity • Pancytopenia and ulcerated lesions on the tongue are typical of disseminated histoplasmosis • Erythema nodosum may occur in immunocompetent people • Diagnosis can be done with microscopic examination of tissue biopsy specimens or bone marrow aspirates (show yeast cells within macrophages), with culture (shows hyphae with macroconidia at 25°C and yeast at 37°C), and serologic tests • No therapy is needed in asymptomatic or mild primary infections • Oral itraconazole is effective against progressive lung disease, and parenteral itraconazole or amphotericin B is the treatment of choice in disseminated disease • Fluconazole is often used in meningitis because it penetrates the spinal fluid well Blastomyces dermatitidis Blastomyces • Blastomyces dermatitidis causes blastomycosis (a.k.a. North American blastomycosis) • B. dermatitidis is a dimorphic fungus that exists as a mold in soil and as a yeast in tissue - The yeast is round with a doubly refractive wall and a single broad-based bud • This fungus is endemic primarily in the eastern US, where it grows in moist soil and forms hyphae with small pear-shaped conidia • Inhalation of the conidia causes human infection - Asymptomatic or mild cases are rarely recognized - Dissemination may result in ulcerated granulomas of skin, bone, or other sites • Diagnosis can be done microscopically with tissue biopsy specimens (show thick walled yeast cells with single broad-based buds), with culture (shows hyphae with small pear-shaped conidia), or with PCR • Itraconazole is the drug of choice for most patients, but amphotericin B should be used to treat severe disease Paracoccidioides brasiliensis Paracoccidioides • Paracoccidioides brasiliensis causes paracoccidioidomycosis (a.k.a. South American blastomycosis) • P. brasiliensis is a dimorphic fungus that exists as a mold in soil and as a yeast in tissue - The yeast is thick-walled with multiple buds • This fungus grows in the soil and is endemic in rural Latin America, which is the only region where the disease occurs • The spores are inhaled, and early lesions occur in the lungs - Asymptomatic infection is common - Alternatively, oral mucous membrane lesions, lymph node enlargement, and sometimes dissemination to many organs develop • Diagnosis can be done with microscopic examination of pus or tissues (shows yeast cells with multiple buds resembling a “ship captain‘s wheel“), with culture (2-4 weeks produces typical organisms), or with serologic test • The drug of choice is itraconazole taken orally for several months

Answer 12

Candida albicans Candida • Candida albicans, the most important species of Candida, causes thrush, vaginitis, esophagitis, diaper rash, and chronic mucocutaneous candidiasis - It also causes disseminated infections such as right-sided endocarditis (especially in IV drug users), bloodstream infections (candidemia), and endophthalmitis - Other important Candida species include C. glabrata (second most common, th. echinocandins), C. tropicalis (th. same as C. albicans), C. parapsilosis (th. same as C. albicans), C. krusei (th. echinocandins), and C. auris (th. echinocandins) • C. albicans is an oval yeast with a single bud - It is part of the normal flora of mucous membranes of the upper respiratory, gastrointestinal, and female genital tracts - In tissues it appears most often as yeasts or as pseudohyphaes, which are elongated yeasts that visually resemble hyphae - True hyphae are also formed when C. albicans invades tissues • When local or systemic host defenses are impaired, disease may result - Overgrowth of C. albicans in the mouth produces white patches called thrush - Vaginitis with itching and discharge with itching and discharge can occur due to high pH, diabetes, or use of antibiotics - Skin invasion occurs in warm, moist areas, which become red and weeping § Dishwashers in restaurants are commonly affected on fingers and nails § Diaper rash in infants occurs when wet diapers are not changed promptly In immunosuppressed individuals, Candida may disseminate to many organs or cause chronic mucocutaneous candidiasis - IV drug abuse, indwelling IV catheters, and hyperalimentation also predispose to disseminated candidiasis, especially right-sided endocarditis and endophthalmitis (infection within the eye) - Candida esophagitis, often accompanied by involvement of the stomach and small intestine, is seen in patients with leukemia and lymphoma • Diagnosis can be made with microscopic analysis (budding yeast and pseudohyphae appear Gram(+) and can be visualized with calcofluor-white staining), with culture (resemble large staphylococcal colonies, form germ tubes at 37°C), and with a laboratory test that utilizes magnetic resonance technology to detect the presence of yeast DNA and then to identify the species • The drug of choice for most candidal infections is fluconazole, but an echinocandin (e.g. caspofungin, micafungin) can also be used • Treatment of skin infections consists of topical antifungal drugs, such as clotrimazole or nystatin • Disseminated infection is usually treated with fluconazole or echinocandins, but amphotericin B may also be used Cryptococcus neoformans Cryptococcus • Cryptococcus neoformans causes cryptococcosis, especially cryptococcal meningitis - Cryptococcosis is the most common, life-threatening invasive fungal disease worldwide • C. neoformans is an oval, yeast with a narrow-based bud and surrounded by a wide polysaccharide capsule • This fungus occurs widely in nature and grows abundantly well in soil containing bird (especially pigeon) droppings • Human infection results from inhalation of the organism - Lung infection is often asymptomatic or may produce pneumonia - Disease occurs mainly in patients with reduced cell-mediated immunity, in whom the organism disseminates to the CNS (meningitis) and other organs § Note, however, that roughly half the patients with cryptococcal meningitis fail to show evidence of immunosuppression - Subcutaneous nodules are often seen in disseminated disease • Diagnosis can be made with microscopic analysis of spinal fluid mixed with India ink, showing yeast cells surrounded by a wide, unstained capsule - Stains such as periodic acid-Schiff (PAS stain), methenamine silver, and mucicarmine will also allow the organism to be visualized • Other diagnostic options include culturing, serologic tests, and latex particle agglutination • Combined treatment with amphotericin B and flucytosine is used in meningitis and other disseminated disease Penicillium marneffei • Penicillium marneffei is a dimorphic fungus that causes penicilliosis, a tuberculosis-like disease, in AIDS patients, particularly in Southeast Asian countries such as Thailand - The disease can manifest as fever with or without pulmonary infiltrates, as well as hepatosplenomegaly, lymphadenopathy and skin lesions - Other clinical findings include oropharyngeal lesions in addition to intestinal and musculoskeletal involvement - Fungaemia occurs in 50-64% of patients • It grows as a mold that produces a rose-colored pigment at 25°C but at 37°C grows as a small yeast that resembles H. capsulatum • Bamboo rats are the only other known hosts • The diagnosis is made either by growing the organism in culture or by using fluorescent antibody staining of affected tissue • The treatment of choice consists of amphotericin B for 2 weeks followed by oral itraconazole for 10 weeks (may be needed lifelong) - Untreated penicilliosis is almost uniformly fatal

Answer 13

Apergillus fumigatus, A. flavus Aspergillus • Aspergillus species, especially Aspergillus fumigatus, cause (1) infections of the skin, eyes, ears, and other organs; (2) “fungus ball“ in the lungs; and (3) allergic bronchopulmonary aspergillosis Aspergillus species exist only as molds - They have septate hyphae that form V-shaped branches, with walls that are more or less parallel and conidia that form radiating chains • These molds are widely distributed in nature • Transmission is by airborne conidia that colonize and later invade abraded skin, wounds, burns, the cornea, the external ear, or paranasal sinuses - In immunocompromised persons, it can invade the lungs producing hemoptysis and the brain causing an abscess • Aspergilli can grow in cavities within the lungs, especially cavities caused by tuberculosis, where they produce an aspergilloma (fungus ball) • Allergic bronchopulmonary aspergillosis (ABPA) is a hypersensitivity reaction to the presence of Aspergillus in the bronchi - Patients have asthmatic symptoms and a high IgE titer against Aspergillus antigens, and they cough up brownish bronchial plugs containing hyphae • Aspergillus flavus growing on cereals or nuts produces aflatoxin, which may be carcinogenic or acutely toxic Biopsy specimens show septate, branching hyphae invading tissue, and cultures show colonies with characteristic radiating chains of conidia • Voriconazole is the drug of choice for invasive aspergillosis - Amphotericin B, posaconazole, and caspofungin are alternative drugs Mucormycetes (Zygomycetes) Zygomycosis • Mucormycosis (zygomycosis, phycomycosis) is a disease caused by saphrophytic molds (e.g. Mucor, Rhizopus, and Absidia) found widely in the environment • These organisms are transmitted by airborne asexual spores and invade tissues of patients with reduced host defenses - They proliferate in the walls of blood vessels, particularly of the paranasal sinuses, lungs, or gut, and cause infarction and necrosis of tissue distal to the blocked vessels - Patients with diabetic ketoacidosis, burns, bone marrow transplants, or leukemia are particularly susceptible § Diabetic patients are particularly susceptible to rhinocerebral mucormycosis • In biopsy specimens, organisms are seen microscopically as non-septate hyphae with broad, irregular walls and branches that form more or less at right angles • Cultures, although difficult to grow, show colonies with spores contained within a sporangium • Early diagnosis in combination with treatment consisting of amphotericin B administration and surgical removal of necrotic infected tissue has resulted in some remissions and cures - Posaconazole can also be used • Prophylactic use of voriconazole is an option for those at risk of infection

Answer 14

The most effective antifungal drugs, amphotericin B and the various azoles, exploit the presence of ergosterol in fungal cell membranes that is not found in bacterial or human cell membranes. Another class of antifungal drugs, echinocandins, inhibit the synthesis of β-glucan, which is found in fungal cell walls but not in bacterial cell walls. Alteration of fungal cell membranes 1) Amphotericin B - Used in the treatment of a variety of disseminated fungal diseases - It is a polyene with a series of seven unsaturated double bonds in its macrolide ring structure - Disrupts the cell membrane of fungi because of its affinity for ergosterol (fungicidal) - Fungi resistant to amphotericin B have rarely been recovered from patient specimens - Significant renal toxicity; measurement of serum creatinine levels is used to monitor the dose § Nephrotoxicity is significantly reduced when the drug is administered in liposomes, but liposomal amphotericin B is expensive - Fever, chills, nausea, and vomiting are common side effects 2) Nystatin - Another polyene antifungal agent, which, because of its toxicity, is used only topically for infections caused by the yeast Candida 3) Terbinafine - Blocks ergosterol synthesis by inhibiting squalene epoxidase - Used in the treatment of dermatophyte infections of the skin, fingernails, and toenails. 4) Azoles - Block cytochrome P-450-dependent demethylation of lanosterol, the precursor of ergosterol (fungistatic) - Fluconazole, ketoconazole, voriconazole, posaconazole, and itraconazole are used to treat systemic fungal diseases § Fluconazole: candidal and cryptococcal infections § Ketoconazole: blastomycosis, chronic mucocutaneous candidiasis, coccidioidomycosis, and skin infections caused by dermatophytes § Voriconazole: invasive aspergillosis, prophylaxis for mucormycosis § Posaconazole: oropharyngeal candidiasis, mucormycosis, Candida and Aspergillus prophylaxis in immunocompromised individuals § Itraconazole: histoplasmosis and blastomycosis - Clotrimazole and miconazole are used only topically because they are too toxic to be given systematically § Topical therapy of Candida infections and dermatophytes - Fungi resistant to the azole drugs have rarely been recovered from patient specimens Inhibition of fungal cell wall synthesis 1) Echinocandins - Caspfoungin and micafungin are the most commonly used - Lipopeptides that block fungal cell wall synthesis by inhibiting the enzyme that synthesizes β-glucan (fungicidal against Candida, fungistatic against Aspergillus) - Caspofungin is used for the treatment of disseminated candidiasis and for the treatment of invasive aspergillosis that does not respond to amphotericin B Additional drug mechanisms 1) Griseofulvin - Binds to tubulin in microtubules and may act by preventing the formation of the mitotic spindle - Useful in the treatment of hair and nail infections caused by dermatophytes 2) Pentamidine - Inhibits DNA synthesis by an unknown mechanism - Active against fungi and protozoa - Widely used to prevent or treat pneumonia caused by Pneumocystis jirovecii 3) Fluoropyrimidin - Inhibits DNA or RNA synthesis - Active in vitro against Candida spp. and Cryptococcus spp. - Rapid emergence of resistance limits clinical utility - Most common clinical use is in combination with amphotericin B for cryptococcal infections

Answer 15

Staphylococcus aureus Staphylococcus aureus • Staphylococcus aureus causes abscesses, various pyogenic infections (e.g. endocarditis, septic arthritis, and osteomyelitis), toxic shock syndrome, and food poisoning - It is also one of the most common causes of hospital-acquired pneumonia, septicemia, and surgical wound infections - It is an important cause of skin and soft tissue infections, such as folliculitis, cellulitis, impetigo and conjunctivitis • Staphylococci are spherical gram-positive cocci arranged in irregular grapelike clusters • S. aureus can be differentiated from the other staphylococci on the basis that it produces coagulase, ferments mannitol, hemolyzes RBCs, and produces staphyloxanthin (carotenoid pigment, important virulence factor) • >90% of S. aureus strains contain plasmids that encode β-lactamase, making them resistant to most penicillins - Some strains (e.g. MRSA) are resistant to β-lactamase-resistant penicillins, such as methicillin and nafcillin, by virtue of changes in the penicillin-binding proteins - Strains of S. aureus with intermediate resistance to vancomycin (VISA) and with full resistance to vancomycin (VRSA) have also been detected • S. aureus has several important cell wall components and antigens 1) Protein A – major protein in the cell wall, binds to Fc portion of IgG (prevents activation of complement) 2) Teichoic acids – mediate adherence to mucosal cells, lipoteichoic acids play a role in the induction of septic shock 3) Polysaccharide capsule – 11 serotypes based on the antigenicity of the capsular polysaccharide (types 5 and 8 cause 85% of infections) 4) Surface receptors – for specific staphylococcal bacteriophages 5) Peptidoglycan – endotoxin-like properties • Humans are the reservoir for staphylococci and the nose is the main site of colonization for S. aureus - S. aureus can also be found on the skin, especially of hospital personnel and patients, and in the vagina of ~5% of women - Reduced humoral immunity, diabetes, IV drug use, and chronic granulomatous disease (CGD) predispose to infection • The three clinically important exotoxins of S. aureus are enterotoxin, toxic shock syndrome toxin, and exfoliatin a) Enterotoxin: causes food poisoning (vomiting, watery diarrhea), acts as a superantigen, fairly heat-resistant, resistant to stomach acid and digestive enzymes § The toxin is preformed and hence has a short incubation period (1-8 hours) b) Toxic shock syndrome toxin (TSST): causes toxic shock (especially in tampon-using menstruating women), produced locally and enters the bloodstream to cause toxemia, superantigen § Toxic shock syndrome is characterized by fever, hypotension, rash (sunburn-like, desquamates), and organ involvement (liver, kidney, GI tract, CNS, muscle, or blood) c) Exfoliatin: causes “scalded skin“ syndrome in young children, acts as a protease that cleaves desmoglein in desmosomes –> separation of the epidermis at the granular cell layer § Scalded-skin syndrome is characterized by fever, large bullae, and an erythematous macular rash, with recovery usually within 7-10 days • Several other exotoxins of S. aureus can kill leukocytes (leukocidins) and of these, the two most important are alpha toxin and P-V leukocidin • β-lactamase resistant S. aureus strains can be treated with β-lactamase-resistant penicillins (e.g. nafcillin), some cephalosporins, vancomycin, or a combination of a β-lactamasesensitive penicillin (e.g. amoxicillin) and a β-lactamase inhibitor (e.g. clavulanic acid) • The drug of choice for methicillin-resistant or nafcillin-resistant strains is vancomycin, to which gentamicin is sometimes added • VISA and VRSA strains can be treated with daptomycin or quinupristin-dalfopristin (Synercid) Staphylococcus epidermidis and S. saprophyticus • Staphylococcus epidermidis causes prosthetic valve endocarditis and prosthetic joint infections - It is the most common cause of CNS shunt infections and an important cause of sepsis in newborns as wells as peritonitis in patients with renal failure - Found primarily on the human skin (normal flora) and can enter the bloodstream at the site of IV catheters - Infections are almost always hospital-acquired - Does not produce exotoxins - Vancomycin is the drug of choice • Staphylococcus saprophyticus causes UTIs, especially cystitis - Found primarily on the mucosa of the genital tract in young women - Infections are almost always community-acquired - Does not produce exotoxins - Can be treated with TMP-SMX or a quinolone

Answer 16

Streptococcus pyogenes (GAS) • Streptococcus pyogenes(group A streptococcus) is the leading bacterial cause of pharyngitis and cellulitis - It is an important cause of impetigo, necrotizing fasciitis, and streptococcal toxic shock syndrome - It is also the inciting factor of rheumatic fever and acute glomerulonephritis • Streptococci are spherical gram-positive cocci arranged in chains or pairs • α-Hemolytic streptococci form a green zone around their colonies (incomplete lysis of RBCs), whereas β-hemolytic streptococci form a clear zone around their colonies (complete lysis of RBCs) • There are two important antigens of β-hemolytic streptococci 1) C carbohydrate is located in the cell wall and determines the group of β-hemolytic streptococci 2) M protein protrudes from the outer surface of the cell to block phagocytosis, and also determines the type of group A β-hemolytic streptococci • Most streptococci are part of the normal flora of the human throat, skin, and intestines but produce disease when they gain access to tissues or blood • S. pyogenes causes disease by three mechanisms a) Pyogenic inflammation – induced locally b) Exotoxin production – can cause widespread systemic symptoms § Erythrogenic toxin causes the rash of scarlet fever and has a similar mechanism of action to TSST § Streptolysin O (antigenic) and streptolysin S (not antigenic) cause β-hemolysis, anti-streptolysin O (ASO) titers are used in detection of rheumatic fever § Pyrogenic exotoxin A is responsible for most cases of streptococcal toxic shock syndrome and has the same mode of action as staphylococcal TSST § Exotoxin B is a protease that rapidly destroys tissues, causing necrotizing fasciitis c) Immunologic – cross-reaction of antibody with normal tissue • S. pyogenes produces three important inflammation-related enzymes: (1) hyaluronidase, which degrades hyaluronic acid and facilitates rapid spread in skin infections; (2) streptokinase (fibrinolysin), which activates plasminogen and dissolves fibrin; and (3) DNase (streptodornase), which degrades DNA in exudates or necrotic tissue • Since the culture of S. pyogenes takes at least 18 hours, rapid antigen tests have been developed that can give results in ~10 minutes • Infections are treated with either penicillin or amoxicillin - Erythromycin is used in case of penicillin allergy I decided not to write about the poststreptococcal disease (acute GN, rheumatic fever) since they are also covered in Internal and Pathology. The only thing I want to mention is that the JONES criteria stand for the following: J – joint involvement ♡ – myocarditis N – nodules, subcutaneous E – erythema marginatum S – Sydenham chorea

Answer 17

Strep. pneumoniae, S. viridans Streptococcus pneumoniae • Streptococcus pneumoniae causes pneumonia, bacteremia, meningitis, and infections of the upper respiratory tract such as otitis media, mastoiditis, and sinusitis - It is the most common cause of community-acquired pneumonia, meningitis, sepsis in splenectomized individuals, otitis media, and sinusitis • Pneumococci are gram-positive lancet-shaped cocci arranged in pairs (diplococci) or short chains - On blood agar, they produce α-hemolysis and are lysed by bile or deoxycholate - Their polysaccharide capsule has >85 antigenically distinct types • Humans are the natural hosts for pneumococci, and about 5-50% of the healthy population harbors the organisms in the oropharynx • S.pneumoniae has several virulence factors, the most important of which is the capsular polysaccharide - IgA protease enhances the organism‘s ability to colonize the mucosa of the upper respiratory tract by cleaving IgA - Lipoteichoic acid in the cell wall can induce inflammatory cytokine production - Pneumolysin, the hemolysin that causes α-hemolysis, may also contribute to pathogenesis • Factors that lower resistance and predispose persons to pneumococcal infection include alcohol or drug intoxication, abnormality of the respiratory tract (e.g. viral infections, bronchial obstruction), abnormal circulatory dynamics (e.g. heart failure), splenectomy, and certain chronic diseases such as sickle cell anemia and nephrosis • Aside from microscopic analysis and culture, diagnosis can also be made with rapid latex agglutination • Most pneumococci are susceptible to penicillins and erythromycins, but resistant strains have emerged and can be treated with vancomycin (severe infection) or ceftriaxone (less severe infection) • Two types of vaccines are available, one for children under the age of 5 years and immunocompromised individuals (13-valent pneumococcal conjugate vaccine), and the other for healthy individuals age 50 years or older (23-valent pneumococcal unconjugated vaccine) Viridans group • Viridans group streptococci are the most common cause of infective endocarditis - They enter the bloodstream (bacteremia) from the oropharynx, typically after dental surgery - The signs of endocarditis are fever, heart murmur, anemia, and embolic events such as splinter hemorrhages, subconjunctival petechial hemorrhages, and Janeway lesions - It is 100% fatal unless effectively treated with antimicrobial agents • Streptococcus mutans synthesizes polysaccharides (dextrans) that are found in dental plaque and lead to dental caries • Viridans streptococci, especially S. anginosus, S. milleri, and S. intermedius, also cause brain abscesses, often in combination with mouth anaerobes • Pathogenesis of the viridans streptococci is uncertain, but many produce a glycocalyx that enables the organisms to adhere to the heart valve • Endocarditis caused by most viridans streptococci is curable by prolonged penicillin treatment

Answer 18

Streptococcus agalactiae • Streptococcus agalactiae (group B streptococcus) is the leading cause of neonatal sepsis and meningitis, as well as an important cause of neonatal pneumonia • The main predisposing factor is prolonged (longer than 18 hours) rupture of the membranes in women who are colonized with the organism • Group B streptococci are characterized by their ability to hydrolyze hippurate and by the production of a protein that causes enhanced hemolysis on sheep blood agar when combined with β-hemolysins of S. aureus (CAMP test) • A rapid test is available for the detection of group B streptococci in vaginal and rectal samples, and results are obtained in ~1 hour • The drug of choice is either penicillin G or ampicillin Enterococcus genus • Enterococcus faecalis (group D streptococcus) is an important cause of hospital-acquired urinary tract infections and endocarditis - Indwelling urinary catheters and urinary tract instrumentation are important predisposing factors for UTIs - Patients who have undergone GI or urinary tract surgery or instrumentation are at increased risk of endocarditis caused by enterococci • Enterococci are members of the normal flora of the colon • Group D streptococci hydrolyze esculin in the presence of bile (i.e. they produce a black pigment on bile-esculin agar) Enterococcus - Enterococci can be differentiated from other group D streptococci on the basis that they grow in hypertonic (6.5% NaCl), whereas nonenterococci do not • Enterococcal endocarditis can be eradicated only by a penicillin or vancomycin combined with an aminoglycoside • Enterococci resistant to multiple drugs have emerged (e.g. VRE), and are treated with linezolid and daptomycin Anaerobic streptococci • Peptostreptococci grow under anaerobic or microaerophilic conditions and produce variable hemolysis - They are members of the normal flora of the gut, mouth, and female genital tract and participate in mixed anaerobic infections

Answer 19

• The Neisseria genus contains two important human pathogens: Neisseria meningitidis and Neisseria gonorrhoeae • Neisseria are gram-negative cocci that resemble paired kidney beans N. meningitidis (meningococcus) has a prominent polysaccharide capsule that is antiphagocytic and the basis of meningococcal serotyping (A, B, C, Y, and W-135 are the five most common serotypes) - N. gonorrhoeae (gonococcus) has no polysaccharide capsule but has multiple serotypes based on the antigenicity of its pilus protein (>100 serotypes are known) • The endotoxin of Neisseriae consists of lipooligosaccharide (LOS), in contrast to lipopolysaccharide (LPS) found in enteric gram-negative rods Neisseria meningitidis • Neisseria meningitidis mainly causes meningitis and meningococcemia • Humans are the only natural hosts for meningococci • The organisms are transmitted by airborne droplets; they colonize the membranes of the nasopharynx and become part of the transient flora of the upper respiratory tract - From the nasopharynx, the organism can enter the bloodstream and spread to specific sites, such as the meninges or joints, or be disseminated throughout the body (meningococcemia) • The carriage rate of N. meningitidisis high in people who live in close quarters (e.g. students living on campus, military recruits) • Overall, N. meningitidis ranks second to S. pneumoniae as a cause of meningitis but is the most common cause in persons between the ages of 2 and 18 years • Meningococci have four important virulence factors: a) Polysaccharide capsule – antiphagocytic, immunogen in several vaccines b) Endotoxin – causes fever, shock, and other pathophysiologic changes c) IgA protease – helps the bacteria attach to membranes of the upper respiratory tract by cleaving secretory IgA d) Factor H binding protein (FHBP) – binds Factor H, an inhibitor of C3b, and thereby reduces opsonization of the bacteria; immunogen in group B vaccine • The most severe form of meningococcemia is the life-threatening Waterhouse-Friderichsen syndrome, which is characterized by high fever, shock, widespread purpura, DIC, thrombocytopenia, and adrenal insufficiency • Penicillin G is the treatment of choice, but ceftriaxone can also be used • Rifampin or ciprofloxacin can be used for prophylaxis Neisseria gonorrhoeae • Neisseria gonorrhoeae causes gonorrhea as well as neonatal conjunctivitis (ophthalmia neonatorum) and pelvic inflammatory disease (PID) • The organism is usually transmitted sexually and causes disease only in humans - Newborns can be infected during birth • Pili constitute one of the most important virulence factors, because they mediate attachment to mucosal cell surfaces and are antiphagocytic - Other virulence factors include endotoxin (LOS), outer membrane proteins, and IgA protease • Gonococci cause both localized infections, usually in the genital tract, and disseminated infections with seeding of various organs via the bloodstream (gonococcal bacteremia) - Gonorrhea in men is characterized primarily by urethritis accompanied by dysuria and purulent discharge - In women, infection is located primarily in the endocervix, causing a purulent vaginal discharge and intermenstrual bleeding (cervicitis) § The most frequent complication in women is an ascending infection of the uterine tubes (salpingitis, PID), which can result in sterility or ectopic pregnancy as a result of scarring of the tubes - Disseminated gonococcal infections usually manifest as arthritis, tenosynovitis, or pustules in the skin • Ceftriaxone is the treatment of choice and, since mixed infections with C. trachomatis are common, azithromycin or doxycycline should be prescribed also

Answer 20

• Escherichia coli is the most common cause of UTIs and gram-negative rod sepsis - It is one of the two important causes of neonatal meningitis and sepsis and the agent most frequently associated with “traveler‘s diarrhea“ (watery diarrhea) - Some strains of E. coli are enterohemorrhagic (EHEC) and cause bloody diarrhea • E. coli is a straight gram-negative rod and the most abundant facultative anaerobe in the colon and feces • It can be distinguished from the two major intestinal pathogens Shigella and Salmonella on the basis that it ferments lactose • E. coli strains are differentiated from each other by different O, H, and K antigens • The reservoir of E. coli includes both humans and animals - UTI is caused by the patient‘s own colonic flora that colonizes the urogenital area - Neonatal meningitis is caused by organisms in the mother‘s birth canal and is acquired during birth - Traveler‘s diarrhea (usually caused by enterotoxigenic E. coli (ETEC)) is acquired by ingestion of food or water contaminated with human feces - Bloody diarrhea (usually caused by E. coli O157:H7) is acquired in undercooked beef, for example, hamburgers • Within the intestinal tract, E. coli adheres to the cells of the jejunum and ileum by means of pili and, once attached, the bacteria can synthesize any of three enterotoxins a) Heat-labile toxin (LT) – stimulates adenylate cyclase via ADP-ribosylation –> cAMP increase –> watery diarrhea b) Heat-stable toxin (ST) – stimulates guanylate cyclase c) Shiga toxin – produced by certain enterohemorrhagic strains, inhibits protein synthesis leading to bloody diarrhea, can cause hemolytic-uremic syndrome (HUS) if it enters the bloodstream § HUS is characterized by hemolytic anemia, thrombocytopenia, and acute renal failure • Certain O serotypes of E. coli preferentially cause UTIs, where they adhere to the urinary tract epithelium by the interaction of pili with specific receptors • Uncomplicated lower UTI can be treated using oral TMP-SMX or nitrofurantoin • Pyelonephritis can be treated with ciprofloxacin or ceftriaxone • E. coli sepsis requires treatment with parenteral antibiotics, e.g. a 3rd gen. cephalosporin such as cefotaxime • Neonatal meningitis is treated with a combination of ampicillin and cefotaxime • Antibiotic therapy is usually not indicated in E. coli diarrheal disease

Answer 21

Salmonella enteritidis, S. typhi Salmonellae are gram-negative rods that do not ferment lactose but do produce H2S–features that are used in their laboratory identification. Clinically, the Salmonella species are often thought of in two distinct categories, namely, the typhoidal species (i.e. those that cause typhoid fever) and the non-typhoidal species (i.e. those that cause enterocolitis and metastatic infections, such as osteomyelitis). Salmonellae causing enteric fever • This category includes S. typhi and S. paratyphi A, B, and C • In typhoid and other enteric fevers, infection begins in the small intestine, but few gastrointestinal symptoms occur - The organisms enter, multiply in the mononuclear phagocytes of Peyer‘s patches, and then spread to phagocytes of the liver, gallbladder, and spleen - This leads to bacteremia, which is associated with the onset of fever and other symptoms that are probably caused by endotoxin • Invasion of the gallbladder can result in the establishment of a carrier state and excretion of the bacteria in the feces for long periods (google ‘Typhoid Mary‘ for a historical example) • S. typhi is transmitted only by humans, but all other Salmonella species have a significant animal in addition to the human reservoir • The onset of illness is slow, with fever and constipation rather than vomiting and diarrhea (as in enterocolitis) predominating - After the first week, as the bacteremia becomes sustained, high fever, delirium, tender abdomen, and enlarged spleen occur - Rose spots (i.e. rose-colored macules on the abdomen) are associated with typhoid fever but occur only rarely - Leukopenia and anemia are often seen - Liver function tests are often abnormal, indicating hepatic involvement - The disease begins to resolve by the third week, but severe complications such as intestinal hemorrhage or perforation can occur • Salmonella species form an alkaline slant and an acid butt, frequently with both gas and H2S (black color in the butt), on TSI agar - S. typhi produces no gas and very little H2S - Proteus organisms produce a similar reaction but are urease-positive, whereas Salmonella are urease-negative - The isolate can be further identified and grouped by the slide agglutination test into serogroup A, B, C, D, or E based on its O antigen • The treatment of choice is either ceftriaxone or ciprofloxacin • Ampicillin or ciprofloxacin should be used in patients who are chronic carriers of S. typhi, but cholecystectomy may be necessary • Two vaccines are available, but they confer limited (50-80%) protection against S. typhi

Answer 22

This category includes the many serotypes of S. enterica, of which S. enterica serotype cholerasuis is the species most involved in metastatic infections • Enterocolitis is characterized by an invasion of the epithelial and subepithelial tissue of the small and large intestines - The organisms penetrate both through and between the mucosal cells into the lamina propria - After an incubation period of 12-48 hours, enterocolitis begins with nausea and vomiting and then progresses to abdominal pain and diarrhea (mild or severe, watery or bloody) - Usually the disease lasts a few days, is self-limited, causes non-bloody diarrhea, and does not require medical care except in very young and very old • In contrast to Shigella enterocolitis, in which the infectious dose is very small, the dose of Salmonella required is much higher (at least 100,000 organisms) • Septicemia accounts for only 5-10% of Salmonella infections and occurs in one of two settings: (1) a patient with an underlying chronic disease (e.g. sickle cell anemia or cancer), or (2) a child with enterocolitis - The symptoms begin with fever but little or no enterocolitis and then proceed to focal symptoms associated with the affected organ - Osteomyelitis, pneumonia, and meningitis are the most common manifestations - Previously damaged tissues, such as infarcts and aneurysms, are the most frequent sites of metastatic abscesses • Salmonellae causing enterocolitis can be transmitted by either human or animal reservoirs - The most frequent animal source is poultry and eggs • The diagnosis is the same as for S. typhi and S. paratyphi (discussed in previous topic) • The treatment of choice for septicemia with metastatic infection is either ceftriaxone or ciprofloxacin

Answer 23

• Shigella species are gram-negative rods that cause enterocolitis, which is often called bacillary dysentery (bloody diarrhea) • Shigellae can be distinguished from salmonellae by three criteria: they produce no gas from the fermentation of glucose, they do not produce H2S, and they are non-motile • All shigellae have O antigens (polysaccharide) in their cell walls, and these antigens are used to divide the genus into groups A, B, C, and D • Shigellae are the most effective pathogens among enteric bacteria, with ingestion of as few as 100 organisms being able to cause disease • Shigellosis is only a human disease and the organisms are transmitted by the fecal-oral route - The four Fs–fingers, flies, food, and feces–are the principle factors in transmission • There is no prolonged carrier state with Shigella infections, unlike that seen with S. typhi infections • Dysentery occurs when the shigellae invade the cells of the mucosa of the distal ileum and colon - Local inflammation accompanied by ulceration occurs, but the organisms rarely penetrate through the wall or enter the bloodstream - After an incubation period of 1-4 days, symptoms begin with fever and abdominal cramps followed by diarrhea, which may be watery at first but later contains blood and mucus - The diarrhea frequently resolves in 2 or 3 days - Although some strains produce an enterotoxin (called Shiga toxin), invasion (mediated by invasion plasmid antigen (Ipa)) is the critical factor in the pathogenesis • The disease varies from mild to severe depending on the species of Shigella and the age of the patient, with young children and elderly people being the most severely affected - Shigella dysenteriae causes the most severe disease - Shigella sonnei causes mild disease • The main treatment for shigellosis is fluid and electrolyte replacement • In severe cases, a fluoroquinolone (e.g. ciprofloxacin) is the drug of choice, with TMP-SMX as an alternative choice in case of resistance

Answer 24

Klebsiella-Enterobacter-Serratia group • These gram-negative rods are usually opportunistic pathogens that cause nosocomial infections, especially pneumonia and UTIs - K. pneumoniae is an important respiratory tract pathogen outside hospitals as well • Klebsiella pneumoniae, Enterobacter cloacae, and Serratia marcescens are the species most often involved in human infections - They are frequently found in the large intestine but are also present in soil and water • Of the three organisms, K. pneumoniae is most likely to be a primary, non-opportunistic pathogen, a property related to its antiphagocytic capsule • Enterobacter and Serratia infections are clearly related to hospitalization, especially to invasive procedures such as IV catheterization, respiratory intubation, and urinary tract manipulations • In addition to the usual clinical manifestations of UTIs and pneumonia, these three bacteria can also be associated with bacteremia and secondary spread to the meninges and liver - Serratia also causes endocarditis in IV drug users • It is difficult to distinguish infections caused by these organisms on clinical grounds, with the exception of Klebsiella pneumonia, which produces a thick, mucoid, bloody sputum (“currant-jelly“ sputum) and can progress to necrosis and abscess formation • Antibiotic sensitivity testing is needed since isolates from hospital-acquired infections are frequently multidrug-resistant • An aminoglycoside (e.g. gentamicin) and a cephalosporin (e.g. cefotaxime) are used empirically until the results of testing are known • In severe Enterobacter infections, a combination of imipenem and gentamicin is often used Proteus mirabilis Proteus-Providencia-Morganella group • These gram-negative rods primarily cause UTIs, both community- and hospital-acquired • They are distinguished from other Enterobacteriaceae by their ability to produce the enzyme phenylalanine deaminase - They also produce the enzyme urease, and certain species produce a striking swarming effect on blood agar due to their high motility • In the past, there were four medically important species of Proteus, but DNA analysis has shown that two of the four were significantly different - Proteus morganii is now Morganella morganii and Proteus rettgeri is now Providencia rettgeri • The organisms are present in the human colon as well as in soil and water • The production of urease is an important feature of the pathogenesis of UTIs, since it forms ammonia from urea in urine and raises the pH, producing alkaline urine - This encourages the formation of stones (calculi) called “struvite“ composed of magnesium ammonium phosphate, and also favors growth of the organisms • The signs and symptoms of UTI caused by these organisms cannot be distinguished from those caused by E. coli or other members of the Enterobacteriaceae • Proteus species can also cause pneumonia, wound infections, and septicemia • Most strains are sensitive to aminoglycosides and TMP-SMX, but in case of antibiotic resistance cephalosporins may be used

Answer 25

Yersinia pestis • Yersinia pestis is the cause of plague, also known as the black death, the scourge of the Middle Ages - It is also a contemporary disease, occurring in the western US and in many other countries around the world • Y. pestisis a small gram-negative rod that exhibits bipolar staining (i.e. it resembles a safety pin, with a central clear area) - It has a polysaccharide-protein complex capsule that is highly linked to its virulence • It is one of the most virulent bacteria known, with only 1-10 organisms being needed to cause disease • Although the plague is endemic in the western US, 99% of cases occur in Southeast Asia • Rodents serve as reservoirs for the disease, with fleas acting as a vector for transmission - Humans are accidental hosts who get infected through flea bites • The organisms inoculated at the time of the bite spread to the regional lymph nodes, which become swollen and tender - These swollen lymph nodes are the buboes that have led to the name bubonic plague - High fever, myalgias, and prostration usually accompany the lymphadenopathy, with septic shock and pneumonia as the main life-threatening subsequent events - The organisms can then spread through the blood (bacteremia) and disseminate to form abscesses in many organs - The endotoxin-related symptoms (e.g. DIC, cutaneous hemorrhages) were probably the genesis of the term black death • In addition to transmission by flea bites, respiratory droplet transmission of the organism from patients with pneumonic plague can occur - Pneumonic plague can arise either from inhalation of an aerosol or from septic emboli that reach the lungs • Untreated bubonic plague is fatal in approximately half of the cases, and untreated pneumonic plague is invariably fatal • Smear and culture of blood or pus from the bubo is the best diagnostic procedure - Giemsa or Wayson stain reveals the typical safety-pin appearance of the organism • The treatment of choice is a combination of streptomycin and a tetracycline (e.g. doxycycline), although streptomycin alone can be used • A vaccine consisting of formalin-killed organisms provides partial protection against bubonic but not pneumonic plague Yersinia enterocolitica and Yersinia pseudotuberculosis • Yersinia enterocolitica and Yersinia pseudotuberculosis are gram-negative, oval rods that are larger than Yersinia pestis • These organisms are transmitted to humans by contamination of food with the excreta of domestic animals such as dogs, cats, and cattle • Y. enterocolitica causes enterocolitis that is clinically indistinguishable from that caused by Salmonella or Shigella - It is usually isolated from stool specimens and forms a lactose-negative colony on MacConkey‘s agar • Both organisms can cause mesenteric adenitis that clinically resembles acute appendicitis • Rarely, these organisms are involved in abscesses of the liver or spleen, mainly in persons with underlying disease • Infection is associated with reactive arthritis and Reiter‘s syndrome • Enterocolitis and mesenteric adenitis caused by these organisms do not require treatment • In case of bacteremia or abscess, either TMP-SMX or ciprofloxacin is usually effective

Answer 26

Vibrio cholerae, V. parahaemolyticus, V. vulnificus Vibrios are curved, comma-shaped, gram-negative rods. Vibrio cholerae • Vibrio cholerae, the major pathogen in this genus, is the cause of cholera • It is divided into two groups according to the nature of its O cell wall antigen - O1: epidemic disease § This group is further divided into two biotypes (classic and El Tor) and three serotypes (Ogawa, Inaba, and Hikojima) - non-O1: sporadic disease or non-pathogens • Vibrio cholerae is transmitted by fecal contamination of water and food, primarily from human sources - The main animal reservoirs are marine shellfish, such as shrimp and oysters • Human carriers are frequently asymptomatic • The pathogenesis of cholera is dependent on colonization of the small intestine by the organism and secretion of an enterotoxin called choleragen (cholera toxin) - Cholera toxin stimulates adenylate cyclase via ADP-ribosylation and causes an increase in cAMP , resulting in a massive watery diarrhea (“rice-water stool“) - Morbidity and death are due to dehydration and electrolyte imbalance - If treatment is instituted promptly, the disease is self-limited and resolves in ~7 days • The organism is particularly sensitive to stomach acid, so large numbers of bacteria must be ingested for disease to occur • The watery diarrhea is not accompanied by abdominal pain, and subsequent symptoms are referable to the marked dehydration - Loss of fluid and electrolytes leads to cardiac and renal failure - Acidosis and hypokalemia also occur as a result of loss of bicarbonate and potassium in the stool - Mortality rate without treatment is 40% • A culture of the diarrhea stool containing V. cholerae will show colorless colonies on MacConkey‘s agar because lactose is fermented slowly • On TSI agar, an acid slant and an acid butt without gas or H2S are seen because the organism ferments sucrose • Treatment consists of prompt, adequate replacement of water and electrolytes (either orally or IV), without the need for antibiotics (although tetracycline does shorten the duration of symptoms) Vibrio parahaemolyticus • Vibrio parahaemolyticus is a marine organism transmitted by ingestion of raw or undercooked seafood, especially shellfish such as oysters • It is a major cause of diarrhea in Japan, where raw fish is eaten in large quantities • Little is known about its pathogenesis, except that an enterotoxin similar to cholera toxin is secreted and limited invasion sometimes occurs • The clinical picture varies from mild to quite severe watery diarrhea, nausea and vomiting, abdominal cramps, and fever • The illness is self-limited, lasting about 3 days • V. parahaemolyticusis distinguished from V. cholerae mainly on the basis of growth in NaCl, since the former can grow in 8% NaCl solution (since it is halophilic) whereas the latter cannot • No specific treatment is indicated, because the disease is relatively mild and self-limited Vibrio vulnificus • Vibrio vulnificus is also a marine organism • It causes severe skin and soft tissue infections (cellulitis), especially in shellfish handlers who often sustain skin wounds • It can also cause a rapidly fatal septicemia in immunocompromised people who have eaten raw shellfish containing the organism • Hemorrhagic bullae in the skin often occur in patients with sepsis caused by V. vulnificus • Chronic liver disease predisposes to severe infections • The recommended treatment is doxycycline

Answer 27

Haemophilus influenzae • Haemophilus influenzae used to be the leading cause of meningitis in young children, but the use of the highly effective conjugate vaccine has greatly reduced its incidence - It is still an important cause of respiratory tract infections (otitis media, sinusitis, conjunctivitis, and epiglottitis) and sepsis in children - It also causes pneumonia in adults, particularly in those with COPD • H. influenzae is a small gram-negative rod with a polysaccharide capsule - Unencapsulated strains can also cause disease but are usually noninvasive • Of the six serotypes, distinguished on the basis of the antigenicity of the capsular polysaccharide, type b is the most important • H. influenzae infects only humans - It enters the body by the inhalation of airborne droplets into the respiratory tract, resulting in either asymptomatic colonization or infections - After becoming established in the upper respiratory tract, the organism can enter the bloodstream (bacteremia) and spread to the meninges - Other serious infections caused by this organism include septic arthritis, cellulitis, sepsis, and epiglottitis • The organism produces an IgA protease that degrades secretory IgA, thus facilitating attachment to the respiratory mucosa • Most infections occur in children between the ages of 6 months and 6 years, with a peak in the age group from 6 months to 1 year • Laboratory diagnosis depends on isolation of the organism on chocolate agar enriched with factor X (a heme compound) and factor V (NAD) - Definitive identification can be made with either biochemical tests or the capsular swelling (quellung) reaction • Untreated H. influenzae meningitis has a fatality rate of approximately 90% • The treatment of choice for severe infections by H. influenzae is ceftriaxone, but less severe upper respiratory tract infections are treated with either amoxicillin-clavulanate or TMP-SMX • The vaccine contains the capsular polysaccharide of H. influenzae type b conjugated to diphtheria toxoid or other carrier protein and is given between the ages of 2 and 15 months Haemophilus ducreyi • Haemophilus ducreyi is a small gram-negative rod that causes the sexually transmitted disease chancroid (soft chancre), which is common in tropical countries • The disease begins with painful penile lesions, non-indurated (soft) ulcers, and local lymphadenitis (bubo) • The diagnosis is made by isolating H. ducreyi from the ulcer or from pus aspirated from a lymph node and growing it on a chocolate agar supplemented with factor X • Chancroid can be treated with erythromycin, azithromycin, or ceftriaxone Gardnerella vaginalis • Gardnerella vaginalis is the main organism associated with bacterial vaginosis, the most common vaginal infection of sexually active women • G. vaginalis is a small, facultative gram-variable rod (i.e. some organisms are purple while others are pink in a Gram-stained specimen) - Structurally, it has a gram-positive cell wall but the wall is thin • The pathogenesis of bacterial vaginosis is uncertain, but it is not considered to be a sexually transmitted infection • Bacterial vaginosis is characterized by a malodorous white or gray-colored vaginal discharge that has a characteristic “fishy“ odor - Inflammatory changes are typically absent - Mild itching may occur - Women with bacterial vaginosis have a higher incidence of preterm deliveries • Clue cells, which are vaginal epithelial cells covered with bacteria, are an important laboratory finding seen in microscopic examination of the vaginal discharge - In addition, the “whiff“ test, which consists of treating the vaginal discharge with 10% KOH and smelling a pungent “fishy“ odor, is often positive - A pH of >4.5 of the vaginal discharge supports the diagnosis of bacterial vaginosis • The drug of choice is metronidazole

Answer 28

Pseudomonas aeruginosa Pseudomonas • Pseudomonas aeruginosa causes infections (e.g. sepsis, pneumonia, and UTIs) primarily in patients with lowered host defenses - It also causes chronic lower respiratory tract infections in patients with cystic fibrosis, wound infections (cellulitis) in burn patients, and malignant otitis externa in diabetic patients • Pseudomonads are gram-negative aerobic rods • Pseudomonads are able to grow in water containing only traces of nutrients (e.g. tap water) and this favors their persistence in the hospital environment - They are also remarkably resistant to disinfectants • P. aeruginosa produces two pigments useful in clinical and laboratory diagnosis: (1) pyocyanin, which can color the pus in a wound blue, and (2) pyoverdin (fluorescein), a yellow-green pigment that fluoresces under UV light • The organism is found chiefly in soil and water, although ~10% of people carry it in the normal flora of the colon • P. aeruginosa is primarily an opportunistic pathogen that causes nosocomial infections • The best known exotoxin of P. aeruginosa is exotoxin A, which causes tissue necrosis via ADP-ribosylation of elongation factor-2 (EF-2) - It also produces enzymes, such as elastase and proteases that are histotoxic and facilitate invasion of the organism into the bloodstream • Strains of P. aeruginosa that have a type III secretion system1 are significantly more virulent than those that do not • P. aeruginosa can cause a variety of infections in addition to its already mentioned main manifestations (pneumonia, UTI, wound infections) - Spread to the skin can cause black, necrotic lesions called ecthyma gangrenosum - It is an important cause of endocarditis in IV drug users - Severe external otitis (malignant otitis externa) and other skin lesions (e.g. folliculitis) occur in users of swimming pools and hot tubs (hot tub folliculitis) in which chlorination is inadequate - It is the most common cause of osteomyelitis of the foot in those who sustain puncture wounds through the soles of gym shoes - Corneal infections caused by P. aeruginosa are seen in contact lens users • Patients with P. aeruginosa sepsis have a mortality rate of >50% • A typical metallic sheen of the growth on TSI agar, coupled with the blue-green pigment on ordinary nutrient agar and a fruity aroma are sufficient to make a presumptive diagnosis • Because P. aeruginosa is resistant to many antibiotics, treatment must be tailored to the sensitivity of each isolate and monitored frequently - Treatment of choice: piperacillin/tazobactam plus an aminoglycoside (e.g. gentamicin or amikacin) - Ceftazidime is also effective - Highly-resistant strains: colistin (polymixin E) - UTI: ciprofloxacin Acinetobacter • Acinetobacter species are small coccobacillary gram-negative rods found commonly in soil and water, but they also colonize the skin and upper respiratory tract • They are opportunistic pathogens that readily colonize patients with compromised host defenses • Acinetobacter baumannii, the species usually involved in human infection, causes disease chiefly in a hospital setting usually associated with respiratory therapy equipment (ventilator-associated pneumonia) and indwelling catheters (UTI) • Laboratory diagnosis is made by culturing the organism • A. baumannii is remarkably antibiotic resistant, and some isolates are resistant to all known antibiotics • Imipenem is the drug of choice for antibiotic-susceptible strains, whereas colistin is useful in carbapenem-resistant strains Burkholderia • Burkholderia mallei is a gram-negative rod that causes glanders in horses and is transmissible to humans - Transmission is mostly via direct contact with infected animals (through abraded skin or mucous membranes), inhalation, or ingestion of the organism - Veterinarians, grooms, horsemen, butchers, and lab workers are at risk of infection - The disease is endemic to parts of Africa, the Middle East, Asia, and South America - There are four types of glanders disease in humans 1) Cutaneous – erythema, ulceration, lymphadenopathy, 20% mortality 2) Pulmonary – pneumonia, pulmonary abscesses, pleural effusion, 90-95% mortality if untreated, 40% mortality if treated 3) Septicemic – fever, chills, myalgia, chest pain, rash, tachycardia, jaundice, photophobia, >95% fatality if untreated, >50% mortality if treated 4) Chronic – multiple abscesses in muscles, joints, spleen, liver; weight loss; lymphadenopathy; 50% mortality if treated; can last up to 25 years - Diagnosis is based on culturing, gram-staining (safety-pin appearance), and serology - Treatment is with carbapenems • Burkholderia pseudomallei (also known as Pseudomonas pseudomallei) is a gram-negative rod that causes melioidosis, a rare disease found primarily in Southeast Asia - The organism is found in soil and is transmitted most often when soil contaminates skin abrasions - The acute disease is characterized by high fever and bloody, purulent sputum, and untreated cases can proceed to sepsis and death - In the chronic form, the disease can appear as pneumonia or lung abscess and may resemble tuberculosis - Diagnosis is made by culturing the organism from blood or sputum - The treatment of choice is ceftazidime, aminoglycosides, or TMP-SMX • Burkholderia cepacia (formerly known as Pseudomonas cepacia) is an important cause of chronic infection in patients with cystic fibrosis Stenotrophomonas • Stenotrophomonas maltophilia (formerly known as Xanthomonas maltophilia, and before that as Pseudomonas maltophilia) is a gram-negative rod that causes nosocomial and opportunistic infections similar to P. aeruginosa (pneumonia, UTI, skin and wound infections, sepsis) • Diagnosis is based on culture, biochemical reactions, and MALDI TOF • Treatment is with fluoroquinolones

Answer 29

Legionella pneumophila • Legionella pneumophila (and other legionellae) causes pneumonia, both in community and in hospitalized immunocompromised patients • Legionellae are gram-negative rods that stain faintly with the standard Gram stain - They do, however, have a gram-negative type of cell wall • L. pneumophila causes ~90% of pneumonia attributed to legionellae Legionellae are associated chiefly with environmental water sources such as air conditioners and water-cooling towers • The portal of entry is the respiratory tract, and pathologic changes occur primarily in the lung - The clinical picture can vary from mild influenza-like illness (Pontiac fever) to severe pneumonia accompanied by mental confusion, non-bloody diarrhea, proteinuria, and microscopic hematuria - Although cough is a prominent symptom, sputum is frequently scanty and nonpurulent - Hyponatremia (serum Na+ <130 mEq/l) is an important laboratory finding in Legionella pneumonia - Most cases resolve spontaneously in 7-10 days, but the infection might be fatal in vulnerable patients • In severe cases, bacteremia occurs, accompanied by damage to the vascular endothelium in multiple organs, especially the brain and kidneys • The major virulence factor of the organism is endotoxin (LPS), no exotoxins are produced • The typical candidate for Legionnaires‘ disease is an older man who smokes and consumes substantial amounts of alcohol - Patients with AIDS, cancer, or transplants (especially renal) or patients on corticosteroids are also predisposed to Legionella pneumonia • Despite airborne transmission of the organism, person-to-person spread does not occur • Azithromycin or erythromycin (with or without rifampin) is the treatment of choice - Certain fluoroquinolones (e.g. levofloxacin, trovafloxacin) are also drugs of choice Listeria monocytogenes • Listeria monocytogenes causes meningitis and sepsis in newborns, pregnant women, and immunosuppressed adults - It also causes outbreaks of febrile gastroenteritis and is a major cause of concern for the food industry • L. monocytogenes is a small gram-positive rod arranged in V- or L-shaped formations similar to corynebacteria - The organism exhibits an unusual tumbling movement that distinguishes it from the corynebacteria, which are non-motile • Listeria grows well at cold temperatures (“cold enhancement“), so storage of contaminated food in the refrigerator can increase the risk of gastroenteritis • Listeria infections occur primarily in two clinical settings: (1) in the fetus or in a newborn as a result of transmission across the placenta or during delivery; and (2) in pregnant women and immunosuppressed adults, especially renal transplant patients • The organism is distributed worldwide in animals, plants and soil - From these reservoirs, it is transmitted to humans primarily by ingestion of unpasteurized milk products, undercooked meat, and raw vegetables § Contact with infected farm animals and their feces is also an important source • Following ingestion, the bacteria appear in the colon and then can colonize the female genital tract • The pathogenesis of Listeria depends on the organism‘s ability to invade and survive within cells - Invasion is mediated by internalin made by Listeria and E-cadherin on human cells - Upon entering the cell, the organism produces listeriolysin, which allows it to escape from the phagosome into the cytoplasm - It can then move from cell to cell by means of actin rockets–filaments of actin polymerize and propel the bacteria through the membrane of one human cell and into another • Infection during pregnancy can cause abortion, premature delivery, or sepsis during the peripartum period • Newborns infected at the time of delivery can have acute meningitis 1-4 weeks later • Gastroenteritis caused by L. monocytogenes is characterized by watery diarrhea, fever, headache, myalgias, and abdominal cramps but little vomiting • Laboratory diagnosis is primarily by Gram stain and culture - The gram-positive rods resemble diphtherioids and form small gray, colonies with a narrow zone of β-hemolysis on blood agar plate • Treatment of invasive disease, such as meningitis and sepsis, consists of TMP-SMX - Combinations, such as ampicillin and gentamicin or ampicillin and TMP-SMX, can also be used

Answer 30

Brucella • Brucella species cause brucellosis (undulant fever) • Brucellae are small gram-negative rods without a capsule • The three major human pathogens and their animal reservoirs are Brucella melitensis (goats and sheep), Brucella abortus (cattle), and Brucella suis (pigs) • The organisms enter the body either by ingestion of contaminated milk products or through skin by direct contact in an occupational setting - They localize in the reticuloendothelial system (lymph nodes, liver, spleen, bone marrow), where many organisms are killed by macrophages - Some organisms survive within macrophages and induce a granulomatous reaction, which can progress to form focal abscesses • After an incubation period of 1-3 weeks, nonspecific symptoms such as fever, chills, fatigue, malaise, anorexia, and weight loss occur in an acute or gradual manner - The undulating (rising-and-falling) fever pattern that gives the disease its name occurs in a minority of patients - Enlarged lymph nodes, liver, and spleen are frequently found as well as pancytopenia - Osteomyelitis is the most frequent complication • B. melitensis infections tend to be more severe and prolonged, whereas those caused by B. abortus are more self-limited • Secondary spread from person to person is rare • The organism can be presumptively identified after culture by using a slide agglutination test with Brucella antiserum, and the species can be identified by biochemical tests - If the organisms are not isolated, analysis of a serum sample from the patient for a rise in antibody titer to Brucella can be used to make a diagnosis • The treatment of choice is tetracycline plus rifampin Francisella tularensis Francisella tularensis • Francisella tularensis causes tularemia • F. tularensis is a small, pleomorphic gram-negative rod with a single serologic type - There are two biotypes: type A is more virulent and found primarily in the US, whereas type B is less virulent and found primarily in Europe • F. tularensis has been isolated from >100 different species of wild animals, the most important of which are rabbits, deer, and a variety of rodents - The bacteria are transmitted among these animals by vectors such as ticks, mites, and lice, especially the Dermacentor ticks that feed on the blood of wild rabbits - Humans are accidental “dead-end“ hosts who acquire the infection most often by being bitten by the vector or by having skin contact with the animal during removal of the hide § After entering through the skin, it localizes to the cells of the reticuloendothelial system, and granulomas are formed § Rarely, the organism is ingested in infected meat (causing gastrointestinal tularemia) or inhaled (causing pneumonia) § There is no person-to-person spread • Symptoms are caused primarily by endotoxin, and no exotoxins have been identified • Presentation can vary from sudden onset of an influenza-like syndrome to prolonged onset of a low-grade fever and adenopathy - ~75% of cases are the “ulcero-glandular“ type, in which the site of entry ulcerates and the regional lymph nodes are swollen and painful - Other, less frequent forms of tularemia include glandular, oculoglandular, typhoidal, gastrointestinal, and pulmonary • Disease usually confers lifelong immunity • The most frequently used diagnostic method is the agglutination test with acute- and convalescent-phase serum samples • Streptomycin is the drug of choice • There is a live, attenuated bacterial vaccine that is given only to persons, such as fur trappers, whose occupation brings them into close contact with wild animals

Answer 31

Bordetella pertussis is a small, coccobacillary, encapsulated gram-negative rod that causes whooping cough (pertussis) • B. pertussis, a pathogen only for humans, is transmitted by airborne droplets produced during the severe coughing episodes - The organisms attach to the ciliated epithelium of the upper respiratory tract but do not invade the underlying tissue • Pertussis is a highly contagious disease that occurs primarily in infants and young children and has a worldwide distribution • Several factors play a role in the pathogenesis of pertussis: 1) Attachment of the organism to the cilia of the epithelial cells is mediated by a protein on the pili called filamentous hemagglutinin 2) Pertussis toxin stimulates adenylate cyclase via ADP-ribosylation and thereby elevates cAMP levels, resulting in edema of the respiratory mucosa that contributes to the severe cough of pertussis - It also causes lymphocytosis in the blood of the patient by inhibiting lymphocytes from entering the lymphoid tissue 3) The organisms also synthesize and export adenylate cyclase, which can inhibit the bactericidal activity of phagocytic cells 4) Tracheal cytotoxin is a fragment of the bacterial peptidoglycan that damages ciliated cells of the respiratory tract • Whooping cough is an acute tracheobronchitis that begins with mild upper respiratory tract symptoms followed by a severe paroxysmal cough, which lasts from 1-4 weeks - Despite the severity of the symptoms, the organism is restricted to the resp. tract - Although CNS anoxia and exhaustion can occur as a result of the severe coughing, death is mainly due to pneumonia - In adults, B. pertussis infection manifests as a paroxysmal cough of varying severity lasting weeks • The organism can be isolated from nasopharyngeal swabs taken during the paroxysmal stage and identification of the organism can be made by agglutination with specific antiserum or by fluorescent-antibody staining - PCR tests are also an option when available, as well as serologic tests • Azithromycin is the drug of choice, and supportive care (e.g. oxygen therapy and suction of mucus) might also be needed in the paroxysmal stage • There are two types of vaccines: a) Acellular vaccine § Contains five purified antigens § The main immunogen is pertussis toxoid § Usually given combined with diphtheria and tetanus toxoid (DTaP) in three doses beginning at 2 months of age b) Killed vaccine § Contains inactivated B. pertussis organisms § No longer used in the US due to suspected side effects (e.g. postvaccine encephalopathy)

Answer 32

Bacillus anthracis * Bacillus anthracis causes anthrax, which is common in animals but rare in humans - Human disease occurs in three main forms: cutaneous, pulmonary (inhalation), and gastrointestinal * B. anthracis is a large gram-positive rod with square ends, frequently found in chains - Its antiphagocytic capsule is composed of D-glutamate - It is non-motile, whereas other members of the genus are motile * Spores of the organism persist in soil for years, and humans are most often infected cutaneously at the time of trauma to the skin - Spores can also be inhaled into the respiratory tract and cause pulmonary (inhalation) anthrax § The disease is not communicable from person to person since the organism moves rapidly to the mediastinal lymph nodes - Gastrointestinal anthrax occurs when contaminated meat is ingested * Pathogenesis is based primarily on the production of two exotoxins, that are collectively known as anthrax toxin a) Edema factor is an adenylate cyclase that causes an intracellular increase in cAMP concentration, leading to edema b) Lethal factor is a protease that cleaves the phosphokinase that activates the MAP kinase pathway, inhibiting cell growth * The typical lesions of cutaneous anthrax is a painless ulcer with a black eschar (crust, scab) and striking local edema - The lesion is called malignant pustule Untreated cases progress to bacteremia and death * Pulmonary (inhalation) anthrax, also known as “wool-sorter‘s disease“, begins with nonspecific respiratory tract symptoms resembling influenza, especially a dry cough and substernal pressure - This rapidly progresses to hemorrhagic mediastinitis, bloody pleural effusions, septic shock, and death * The symptoms of gastrointestinal anthrax include vomiting, abdominal pain, and bloody diarrhea * Rapid diagnosis can be performed in special laboratories using PCR-based assays or a direct fluorescent antibody test * Serologic tests, such as ELISA, require acute and convalescent serum samples and can only be used to make a diagnosis retrospectively * Ciprofloxacin is the drug of choice, with doxycyline as an alternative * People at high risk can be immunized with cell-free vaccine containing purified protective antigen (B subunit of exotoxins) as immunogen, but the vaccine is only weakly immunogenic Bacillus cereus * Bacillus cereus causes food poisoning * Spores on grains such as rice survive steaming and rapid frying, and the spores germinate when rice is kept warm for many hours (e.g. reheated fried rice) * The portal of entry is the gastrointestinal tract * B. cereus produces two enterotoxins: one that ADP-ribosylates adenylate cyclase and another that acts as a superantigen * There are two syndromes: (1) One syndrome has a short incubation period (4 hours) and consists primarily of nausea and vomiting, similar to staphylococcal food poisoning (2) The other has a long incubation period (18 hours) and features watery diarrhea, resembling clostridial gastroenteritis * Laboratory diagnosis is usually not done and only symptomatic treatment is given

Answer 33

All Clostridia are anaerobic, spore-forming, gram-positive rods * Gas gangrene can be caused by Clostridium perfringens, Clostridium histolyticum, Clostridium septicum, Clostridium novyi, and Clostridium sordelli - Of these, C. perfringens is the most important pathogen * C. perfringens spores are located in the soil - Vegetative cells are members of the normal flora of the colon and vagina * Gas gangrene is associated with war wounds, automobile and motorcycle accidents, and septic abortions (endometritis) * Organisms grow in traumatized tissue (especially muscle) and produce a variety of toxins - The most important is alpha toxin (lecithinase), which damages cell membranes, including those of RBCs, resulting in hemolysis - Degradative enzymes produce gas in tissues * Pain, edema, cellulitis, and gangrene (necrosis) occur in the wound area - If crepitus is palpated in the affected tissue, it indicates gas in the tissue - The gas is typically hydrogen produced by the anaerobic bacteria - Hemolysis and jaundice are common, as are blood-tinged exudates - Shock and death can ensue, and mortality rates are high * Treatment involves administration of penicillin G and debridement of wounds

Answer 34

Clostridium tetani * Clostridium tetani causes tetanus * Spores are widespread in soil * The portal of entry is usually a wound site (e.g. where a nail penetrates the foot), but the spores can also be introduced during “skin-popping“, a technique used by drug addicts to inject drugs into the skin - Germination of spores is favored by necrotic tissue and poor blood supply in the wound * Neonatal tetanus, in which the organism enters through a contaminated umbilicus or circumcision wound, is a major problem in some developing countries * Tetanus toxin (tetanospasmin) is an exotoxin produced by vegetative cells at the wound site - This polypeptide protease toxin is carried intra-axonally (retrograde) to the CNS, where it binds to ganglioside receptors and blocks release of inhibitory mediators (e.g. glycine and GABA) at spinal synapses * Tetanus is characterized by strong muscle spasms (spastic paralysis, tetany) - Specific clinical features include lockjaw (trismus), a characteristic grimus known as risus sardonicus, and exaggerated reflexes - Opisthotonos, a pronounced arching of the back due to spasm of the strong extensor muscles of the back, is often seen - Respiratory failure ensues due to spasm of the respiratory muscles - A high mortality rate is associated with this disease * There is no microbiologic or serologic diagnosis and the organisms are rarely isolated from the wound site * Tetanus immune globulin (tetanus antitoxin) is used to neutralize the toxin * The role of antibiotics is uncertain, but if they are used either metronidazole or penicillin G can be given * Benzodiazepines should be given to prevent spasms, and respiratory support should be administered * Tetanus is prevented by immunization with tetanus toxoid in childhood and every 10 years after - Usually given in combination with diphtheria toxoid and the acellular pertussis vaccine (DTaP) * When trauma occurs, the wound should be cleaned and debrided, and tetanus toxoid booster should be given Clostridium botulinum * Clostridium botulinum causes botulism * Spores are widespread in soil, contaminate vegetables and meats - When these foods are canned or vacuum-packed without adequate sterilization, spores survive and germinate in the anaerobic environment - Toxin is produced within the canned food and ingested preformed § The toxin is relatively heat-labile and is inactivated by boiling for several minutes - The highest risk foods are alkaline vegetables (green beans, peppers, mushrooms) and smoked fish * Botulinum toxin is absorbed from the gut and carried via the blood to peripheral nerve synapses, where it blocks the release of acetylcholine - It is a protease that cleaves the proteins involved in acetylcholine release - There are eight immunologic types of toxin; types A, B, and E are the most common in human illness * Descending weakness and paralysis, including diplopia, dysphagia, and respiratory muscle failure, are seen * Two special clinical forms occur in addition to the usual ingestion of preformed toxin (1) Wound botulism – spores contaminate a wound, germinate, and produce toxin at the site § Associated with drug abuse, especially skin-popping with black tar heroin (2) Infant botulism – organisms grow in the gut and produce the toxin there § Ingestion of honey containing the organisms is implicated in transmission of infant botulism * Mouse inoculation can be used to detect the toxin in uneaten food and the patient‘s serum - ELISA and PCR tests are being developed * The heptavalent antitoxin against seven types (A-G) of botulinum toxin is the preferred treatment, in addition to respiratory support * Infant botulism is treated with a bivalent antitoxin (A and B) purified from plasma of humans to avoid serum sickness

Answer 35

Clostridium difficile * Clostridium difficile causes antibiotic-associated pseudomembranous colitis and is the most common nosocomial cause of diarrhea * The organism colonizes the large intestine of approximately 3% of the general population and up to 30% of hospitalized patients * It is transmitted by the fecal-oral route, and either spores or the bacterial organism itself can be transmitted * The majority of cases occur in hospitalized patients but about 1/3 are community-acquired * Antibiotics suppress drug-sensitive members of the normal flora of the colon, allowing C. difficile to multiply and produce exotoxins A and B - Clindamycin was the first antibiotic to be recognized as a cause of pseudomembranous colitis, but many antibiotics are known to cause this disease - Cancer chemotherapy also predisposes to pseudomembranous colitis * Pseudomembranous colitis is characterized by diarrhea associated with pseudomembranes (yellow-white plaques) - The diarrhea is usually non-bloody and contains neutrophils in about 50% of cases - Fever and abdominal pain often occur - The organisms rarely enter the bloodstream and rarely cause metastatic infection - Toxic megacolon can occur and surgical resection of the colon may be necessary * Even with adequate treatment, the organism may not be eradicated from the colon and recurrences occur at a rate of ~15-20% * Detection of the exotoxins in the patient‘s stool via ELISA or PCR test is sufficient for diagnosis * The causative antibiotic should be withdrawn and oral metronidazole or vancomycin as well as fluid replacement should be administered Clostridium perfringens * In addition to causing gas gangrene, C. perfringens can also cause food poisoning if ingested into the gastrointestinal tract * Spores are located in soil and can contaminate food - The heat-resistant spores survive cooking and germinate, growing to large numbers in reheated foods (especially meat dishes) * C. perfringens is a member of the normal flora in the colon but not in the small bowel, where the enterotoxin acts to cause diarrhea - The enterotoxin acts as a superantigen * The disease has an 8-16 hour incubation period and is characterized by watery diarrhea with cramps and little vomiting, resolving in 24 hours * Laboratory diagnosis is usually not done and only symptomatic treatment is given

Answer 36

Non-spore forming anaerobic bacteria produce no exotoxins and are mostly members of the normal flora. Bacteroides (– rods) * Members of the genus Bacteroides are the most common cause of serious anaerobic infections (e.g. sepsis, peritonitis, and abscess) - Bacteroides fragilis is the most frequent pathogen * Members of the B. fragilis group are predominant organisms in the human colon, numbering ~1011/g of feces, and are found in the vagina of ~60% of women * Because these organisms are part of the normal flora, infections are endogenous and usually arise from a break in the mucosal surface - Peritonitis and localized abscesses are most common, but necrotizing fasciitis and bacteremia with resulting metastatic abscesses occur as well - Predisposing factors such as surgery, trauma, and chronic disease play an important role in pathogenesis - Local tissue necrosis, impaired blood supply, and growth of facultative anaerobes at the site contribute to anaerobic infections * The polysaccharide capsule of B. fragilis is an important virulence factor * Its endotoxin contains a variant lipid A that makes it 1000-fold less active than the typical endotoxin of other gram-negative bacteria * Bacteroides species can be isolated on blood agar plates containing kanamycin and vancomycin to inhibit unwanted organisms * Metronidazole is the drug of choice since B. fragilis organisms are frequently antibioticresistant - Cefoxitin, clindamycin, and chloramphenicol are alternatives - Aminoglycosides are frequently combined to treat facultative gram-negative rods in mixed infections Prevotella (– rods) * Prevotella melaninogenica (formerly known as Bacteroides melaninogenicus) is an important pathogen in anaerobic infections * P. melaninogenica occurs primarily in the oral cavity * It can cause abscesses of the mouth as well as lung abscesses by aspiration of the oral flora * Produce characteristic black colonies on blood agar * The drug of choice is either metronidazole or clindamycin Fusobacterium (– rods) * Fusobacterium species are part of the human normal flora of the mouth, colon, and female genital tract and are isolated from brain, pulmonary, intra-abdominal, and pelvic abscesses * They are frequently found in mixed infections with other anaerobes and facultative anaerobes * Laboratory diagnosis is made by culturing the organism anaerobically * The drug of choice is either penicillin G, clindamycin, or metronidazole Porphyromonas (– rods) * Porphyromonas gingivalis and Porphyromonas endodontalis are found in the normal flora of the mouth * They cause periodontal infections, such as gingivitis and dental abscesses Actinomyces israelii Actinomyces (+ rods) * Actinomyces israelii causes actinomycosis * A. israelii forms part of the normal flora of the oral cavity * After local trauma such as a broken jaw or dental extraction, it may invade tissues and form filaments surrounded by areas of inflammation * The typical lesion of actinomycosis appears as a hard, non-tender swelling that develops slowly and eventually drains pus through sinus tracts - Hard, yellow granules (sulfur granules) composed of a mass of filaments are formed in the pus - In about 50% of cases, the initial lesion involves the face and neck; in the rest, the chest or abdomen is the site * The disease is not communicable * Diagnosis is made by (1) seeing gram-positive branching rods, especially in the presence of sulfur granules, and (2) seeing growth when pus or tissue specimens are cultured under anaerobic conditions * Treatment consists of prolonged administration of penicillin G, coupled with surgical drainage Bifidobacterium (+ rods) * Bifidobacterium eriksonii is found as part of the normal flora in the mouth and GI tract * It occurs in mixed anaerobic infections Eubacterium (+ rods) * Eubacterium species are present in large numbers as part of the normal flora of the human colon * They rarely cause human disease Lactobacillus (+ rods) * Lactobacilli are found as members of the normal flora in the mouth, colon, and female genital tract - In the mouth, they may play a role in the production of dental caries - In the vagina, they are the main source of lactic acid, which keeps the pH low * They are rare causes of opportunistic infection Mobiluncus (+ rods) * Mobiluncus species are associated with bacterial vaginosis in women Propionibacterium (+ rods) * Propionibacteria are found on the skin and in the GI tract * Propionibacterium acnes is part of the normal flora of the skin and can cause catheter and shunt infections - It is also involved in the pathogenesis of acne, a condition that affects more >85% of teenagers Veillonella (– cocci) * Veillonella parvula is part of the normal flora of the mouth, colon, and vagina * It is a rare opportunistic pathogen that causes abscesses of the sinuses, tonsils, and brain, usually in mixed anaerobic infections Peptococcus (+ cocci) * Peptococci resemble staphylococci and are found as members of the normal flora of the mouth and colon * They are also isolated from abscesses of various organs, usually from mixed anaerobic infections Peptostreptococcus (+ cocci) See topic 4, under “Anerobic streptococci“

Answer 37

Campylobacter jejuni * Campylobacter jejuni is a frequent cause of enterocolitis, especially in children - Infection is associated with Guillan-Barré syndrome (ascending paralysis) and reactive arthritis * Campylobacters are curved, gram-negative rods that appear either comma- or S-shaped - They are microaerophilic, growing best in 5% oxygen * Domestic animals such as cattle, chickens, and dogs serve as a source of the organisms for humans * Transmission is usually fecal-oral and occurs when food and water contaminated with animal feces is ingested - Poultry, meat, and unpasteurized milk are commonly involved * Human-to-human transmission occurs but is less frequent than animal-to-human transmission * Enterocolitis caused by C. jejuni begins as watery, foul-smelling diarrhea followed by bloody stools accompanied by fever or severe abdominal pain - Systemic infections, most commonly bacteremia, are caused more often by C. intestinalis * A stool specimen cultured on blood agar containing antibiotics is used for isolating the organism - It is identified by failure to grow at 25°C, oxidase +, and sensitivity to nalidixic acid * Erythromycin or ciprofloxacin is the treatment of choice for enterocolitis, whereas bacteremia is treated with an aminoglycoside Helicobacter pylori * Helicobacter pylori causes gastritis and peptic ulcers - Infection with H. pylori is a risk factor for gastric carcinoma and is linked to MALT lymphomas * Helicobacters are curved gram-negative rods similar in appearance to campylobacters * The natural habitat of H. pylori is the human stomach, and it is probably acquired by ingestion although it has not been isolated from stool, food, water, or animals - Person-to-person transmission probably occurs because there is clustering of infection within families * H. pylori attaches to the mucus-secreting cells of the gastric mucosa - The production of large amounts of ammonia from urea by the organism‘s urease, coupled with an inflammatory response, leads to damage to the mucosa and ulceration § The ammonia also neutralizes stomach acid, which allows the organism to survive - The chronic inflammation induced by the organism is thought to stimulate B-cell proliferation and eventually a B-cell lymphoma (MALT lymphoma) § H. pylori is often found in the MALT lesion, and antibiotic treatment against it often causes the tumor to regress * Gastritis and peptic ulcer are characterized by recurrent pain in the upper abdomen, frequently accompanied by bleeding into the GI tract * The organism can be seen on Gram-stained smears of biopsy specimens of the gastric mucosa and cultured on the same media as campylobacters * The “urea breath“ test is a non-invasive diagnostic test for H. pylori using radiolabeled CO2 * Treatment involves a combination of two antibiotics (e.g. amoxicillin and metronidazole), bismuth salts (Pepto-Bismol), and proton-pump inhibitors

Answer 38

Treponema pallidum * Treponema pallidum causes syphilis * T. pallidum is a spirochete that grows very slowly and has not been grown on bacteriologic media or in cell culture - The medical importance of this is that antibiotics must be present at an effective level for several weeks to kill the organisms and cure the disease * The antigens of T. pallidum induce specific antibodies as well as non-specific antibodies (reagin) * T. pallidum is transmitted from spirochete-containing lesions of skin or mucous membranes of an infected person to other persons by intimate contact - It can also be transmitted from pregnant women to their fetuses - It is a human organism only, there is no animal reservoir * Syphilis occurs worldwide and its incidence is increasing, with many cases going unreported and limiting public health efforts * T. pallidum produces no important toxins or enzymes * The organism often infects the endothelium of small blood vessels, causing endarteritis * In primary syphilis, the spirochetes multiply at the site of inoculation, and a local, nontender ulcer (chancre) usually forms in 2-10 weeks - The ulcer heals spontaneously, but spirochetes spread widely via the bloodstream (bacteremia) to many organs * 1-3 months later, the lesions of secondary syphilis may occur - Often appear as a maculopapular rash, notably on the palms and soles, or as moist papules on skin and mucous membranes - Moist lesions on the genitals are called condylomata lata and are rich in spirochetes (highly infectious) - Constitutional symptoms include low-grade fever, malaise, anorexia, weight loss, headache, myalgias, and generalized lymphadenopathy - Pharyngitis, meningitis, nephritis, and hepatitis may also occur * Some individuals do not show any symptoms of primary and secondary stages, and yet the disease may progress * About 1/3 of primary and secondary cases will “cure“ themselves without treatment, while another 1/3 remains latent - The latent period can be divided into early (lasts for 1-2 years, symptoms can reappear, patients are infectious) and late (can last for many years, no symptoms, patients are not infectious) stages * In the remaining 1/3 of people, the disease progresses to tertiary syphilis - May show granulomas (gummas), especially of skin and bones; CNS involvement, a.k.a. neurosyphilis (e.g. tabes dorsalis, paresis); or cardiovascular lesions (e.g. aortitis, aneurysms of the ascending aorta) - Treponemes are rarely seen at this stage * T. pallidum also causes congenital syphilis by spreading across the placenta - Skin and bone lesions (e.g. Hutchinson‘s teeth, mulberry molars, saber shins, saddle nose, rhagades, snuffles, and frontal bossing) are common - Hepatosplenomegaly, interstitial keratitis, and eight nerve deafness also occur - Fetal infection can also result in stillbirth * Immunity to syphilis is incomplete, so patients with early syphilis who have been treated can contract syphilis again - Patients with late syphilis are relatively resistant to reinfection * There are three important laboratory approaches for diagnosis 1) Microscopy § Spirochetes are demonstrated in the lesions of primary or secondary syphilis by dark field microscopy or by direct fluorescent antibody test § Biopsy specimens obtained from gummas in tertiary syphilis can be treated with histologic stains such as silver stain or fluorescent antibody 2) Nonspecific serologic tests § Involve the use of nontreponemal antigens § Extracts of normal mammalian tissues (e.g. cardiolipin) react with reagin antibodies in serum samples from patients with syphilis § VDRL and rapid plasma reagin (RPR) tests detect these antibodies § These tests are positive in most cases of primary syphilis and the antibody titer decreases with effective treatment § False-positive reactions occur in infections (e.g. leprosy, hepatitis B, infectious mononucleosis), in various autoimmune diseases, and if the antibody titer is too high (prozone phenomenon) 3) Specific serologic tests § In these tests, T. pallidum reacts in immunofluorescence (FTA-ABS)2 or hemagglutination (TPHA, MHA-TP)3 assays with treponemal antibodies in the patient‘s serum § These antibodies arise within 2-3 weeks of infection § The tests remain positive for life after effective treatment and cannot be used to determine the response to treatment or reinfection * Penicillin G is effective in the treatment of all stages of syphilis - A single injection of benzathine penicillin G, a slow-release depot drug, can eradicate T. pallidum and cure early (primary and secondary) syphilis - If the patient is allergic to penicillin, doxycyclin can be used but must be given for prolonged periods to effect a cure - Aqueous penicillin G is given in neurosyphilis in order to reach therapeutic concentration in the CSF - >50% of patients experience the Jarisch-Herxheimer reaction a few hours after treatment of penicillin, which is characterized by influenza-like symptoms and is attributed to the lysis of the treponemes and release of endotoxin-like substances Non-venereal treponematoses * These are infections caused by spirochetes that are virtually indistinguishable from those caused by T. pallidum * They are endemic in populations and transmitted by direct contact * All these infections result in positive results on serologic tests for syphilis * The diseases include bejel in Africa, yaws (caused by T. pallidum subspecies pertenue) in many humid tropical countries, and pinta (caused by T. carateum) in Central and South America * All can be cured by penicillin

Answer 39

Borrelia species are irregular, loosely coiled spirochetes that stain readily with Giemsa and other stains. They can be cultured in bacteriologic media containing serum or tissue extracts. They are transmitted by arthropods. Borrelia burgdorferi * Borrelia burgdorferi causes Lyme disease, the most common tick-borne disease in the US * B. burgdorferi is a flexible, motile spirochete that is transmitted by the Ixodes tick - The main reservoir of the organism consists of small mammals - The tick must feed for 24-48 hours to transmit and infectious dose * Pathogenesis is associated with spread of the organism from the bite site through the surrounding skin followed by dissemination via the blood (bacteremia) to various organs, especially the heart, joints, and CNS * The clinical findings have been divided into three stages (1) Stage 1 (3-30 days after tick bite) § The most common finding is erythema chronicum migrans, an expanding, painless, non-pruritic, erythematous, macular rash that often has a “bullseye“ appearance § Flu-like symptoms may also appear (2) Stage 2 (weeks to months later) § Myocarditis with various forms of heart block occurs § Aseptic meningitis and cranial neuropathies, such as facial nerve palsy (Bell‘s palsy) also occur, in addition to peripheral neuropathies (3) Stage 3 (after a latent phase lasting weeks to months) § Arthritis, usually of the large joints (e.g. knee), is common § Encephalopathy also occurs * Diagnosis is typically made serologically by detecting either IgM antibody or a rising titer of IgG antibody with an ELISA test * The treatment of choice for stage 1 disease or other mild manifestations is either doxycycline or amoxicillin * For more severe forms or late stage disease, ceftriaxone is recommended Borrelia recurrentis and Borrelia hermsii * Borrelia recurrentis, Borrelia hermsii, and several other borreliae cause relapsing fever * During infection, the antigens of these organisms undergo variation, allowing them to escape the specific antibodies and produce relapses of the illness - This can be repeated 3-10 times * Borrelia recurrentis is transmitted from person to person by the human body louse, and humans are the only hosts * Borrelia hermsii and many other Borrelia species are transmitted to humans by soft ticks, having rodents and small animals as their main reservoirs * During infection, the arthropod bite introduces spirochetes, which then multiply in many tissues, producing fever, chills, headaches, and multiple-organ dysfunction * Diagnosis is usually made by seeing the large spirochetes in stained smears of peripheral blood * Tetracycline may be beneficial early in the illness and may prevent relapses Borrelia miyamotoi * Borrelia miyamotoi causes a relapsing fever-like syndrome * It is transmitted by Ixodes ticks * Clinically, the disease begins with an influenza-like syndrome, accompanied by hepatitis and thrombocytopenia with relapsing episodes * Diagnosis is typically made with serology and the treatment of choice is doxycycline and ceftriaxone

Answer 40

Leptospira interrogans * Leptospira are tightly coiled spirochetes with hooked ends * Leptospira interrogans is the cause of leptospirosis, which is common in tropical countries * Leptospiras infect various animals, including rats and other rodents, domestic livestock, and household pets - Animals excrete leptospiras in urine, which contaminates water and soil * Swimming in contaminated water or consuming contaminated food or drink can result in human infection * Human infection results when leptospiras are ingested or pass through mucous membranes or skin - They circulate in the blood and multiply in various organs, producing fever and dysfunction of the liver (jaundice), kidneys (uremia), lungs (hemorrhage, and CNS (meningitis) * The illness is typically biphasic - Fever, chills, intense headache, and conjunctival suffusion (diffuse reddening) appear early in the disease, followed by a short period of resolution of these symptoms as the organisms are cleared from the blood - The second, “immune“, phase is most often characterized by the findings of aseptic meningitis and, in severe cases, liver damage (jaundice) and impaired kidney function * Leptospira stain poorly with dyes and so are not seen by light microscopy, but are seen by dark field microscopy * Diagnosis is usually based on history of possible exposure, suggestive clinical signs, and a marked rise in IgM antibody titers * The treatment of choice is penicillin G * Doxycycline is effective in preventing the disease in exposed persons

Answer 41

* Corynebacterium diphtheriae causes diphtheria * Corynebacteria are gram-positive rods that appear club-shaped (wider at one end) and are arranged in palisades or in a V- or L-shaped formation - The rods have a beaded appearance due to the presence of metachromatic granules * Humans are the only natural host of C. diphtheriae The organism is transmitted by airborne droplets and resides in the upper respiratory tract - It can also infect skin at the site of a pre-existing skin lesion * Diphtheria toxin inhibits protein synthesis by ADP-ribosylation of elongation factor-2 (EF-2) * A local inflammation in the throat, with a fibrinous exudate that forms the tough, adherent, gray pseudomembrane, is characteristic of the disease * There are three prominent complications of diphtheria 1) Extension of the membrane into the larynx and trachea, causing airway obstruction 2) Myocarditis accompanied by arrhythmias and circulatory collapse 3) Nerve weakness or paralysis, especially of the cranial nerves but also of peripheral nerves affecting the muscles of the extremities * Cutaneous diphtheria causes ulcerating skin lesions covered by a gray membrane * Diagnosis involves culturing the organism on Loeffler‘s medium, a tellurite plate, and a blood agar plate - If C. diphtheriae is recovered from the cultures, either animal inoculation or an antibody-based gel diffusion precipitin test is performed to detect toxin production * The treatment of choice is antitoxin, which should be given immediately on the basis of clinical impression - Additional treatment with penicillin G or erythromycin is also recommended * The vaccine for diphtheria contains diphtheria toxoid and is usually given in combination with tetanus toxoid and acellular pertussis vaccine (DTaP vaccine)

Answer 42

Mycobacterium tuberculosis * Mycobacterium tuberculosis causes tuberculosis * M. tuberculosis is an aerobic, acid-fast rod - The term acid-fast refers to an organism‘s ability to retain the carbolfuchsin stain despite subsequent treatment with an ethanol-hydrochloric mixture, and is due to a high lipid content (~60%) in the cell wall * Worldwide, M. tuberculosis causes more deaths than any other single microbial agent - ~1/3 of the world‘s population is infected, 1.7 million deaths/year with 9 million new cases * M. tuberculosis is transmitted from person to person by respiratory aerosols produced by coughing - The source of the organism is a cavity in the lung that has eroded into a bronchus - The portal of entry is the respiratory tract and the initial site of infection is the lung - Humans are the natural reservoir of M. tuberculosis, although some animals (e.g. cattle) can also be infected * The organism preferentially infects macrophages and other reticuloendothelial cells * The disease tuberculosis occurs in only a small number of infected individuals * Primary tuberculosis is the first manifestation of disease and usually results in a Ghon focus in the lower lung, with or without involvement of draining lymph nodes (Ghon complex) - Primary tuberculosis can heal by fibrosis, or it can lead to progressive lung disease (especially in HIV infection and malnutrition - It can also cause bacteremia and miliary tuberculosis, or disseminate via the lymphatics or blood vessels and form dormant tubercle bacilli in several organs (latent tuberculosis) § Latent tuberculosis can reactivate in adult life (secondary tuberculosis), usually forming a cavitary lesion in the upper lung lobes, and can progress to extrapulmonary tuberculosis affecting the CNS (parenchymal tuberculoma or meningitis), vertebral bodies (Pott‘s disease), lymph nodes, kidneys, GI tract, or adrenals * Reactivation is seen primarily in immunocompromised or debilitated patients * There are two types of lesions in tuberculosis (1) Exudative lesions, which consist of an acute inflammatory response and occur chiefly in the lungs at the initial site of infection (2) Granulomatous lesions, which consist of a central area of giant cells containing tubercle bacilli surrounded by a zone of epithelioid cells § A tubercle is a granuloma surrounded by fibrous tissue that has undergone central caseation necrosis * Prior infection can be detected by a positive tuberculin skin test result, which is due to a delayed hypersensitivity reaction * Many organs can be involved in tuberculosis, and therefore the clinical findings can be diverse - Fever, fatigue, night sweats, and weight loss are common - Swollen, non-tender, cervical lymphadenitis (scrofula) and erythema nodosum are also common - Miliary tuberculosis is characterized by multiple disseminated lesions that resemble millet seeds - Tuberculous meningitis and tuberculous osteomyelitis are important disseminated forms - Gastrointestinal tuberculosis is characterized by abdominal pain and diarrhea accompanied by more generalized symptoms of fever and weight loss - Oropharyngeal tuberculosis typically presents as a painless ulcer accompanied by local adenopathy - Renal tuberculosis presents with dysuria, hematuria, and flank pain * The initial diagnostic test is acid-fast staining of sputum or other specimens, followed by culture on Löwenstein-Jensen agar for up to 8 weeks * Multidrug therapy is used to prevent the emergence of drug-resistant mutants during the long (6-9 month) duration of treatment - The treatment consists of isoniazid (INH), rifampin, pyrazinamide, and ethambutol (the details of which can be found in topic #5 in part I) * BCG vaccine can be used to induce partial resistance to tuberculosis - The vaccine contains a strain of live, attenuated M. bovis called bacillus CalmetteGuérin

Answer 43

Mycobacterium leprae * Mycobacterium leprae causes leprosy (Hansen‘s disease) * M. leprae is an aerobic, acid-fast rod that has not been grown in the laboratory * Humans are the natural hosts, although the armadillo can be a reservoir * Due to its preference for lower temperature (30°C), M. leprae preferentially grows in the skin and superficial nerves * M. leprae is the slowest growing human pathogen, with a doubling time of 14 days * Infection is acquired by prolonged contact with patients with lepromatous leprosy, who discharge M. leprae in large numbers in nasal secretions and from skin lesions * The organism replicates intracellularly, typically within skin histiocytes, endothelial cells, and Schwann cells of nerves * There are two distinct forms of leprosy, with several intermediate forms between the two extremes 1) Tuberculoid leprosy § Cell-mediated inflammatory response (CMI) limits growth and granulomas containing giant cells form § The CMI response consists primarily of CD4+ T helper cells and a Th-1 profile of cytokines (INF-γ, IL-2, IL-12) § Nerve damage is caused by the CMI response § Lepromin skin test result is positive § Hypopigmented macular or plaque-like lesions, thickened superficial nerves, and significant anesthesia of the skin lesions occur 2) Lepromatous leprosy § CMI response to the organism is poor § The skin and mucous membrane lesions contain large numbers of organisms as well as foamy histiocytes § The T-cell response consists primarily of Th-2 cells § Nerve damage seems likely to be caused by direct contact to the organisms § Lepromin skin test is negative § Multiple nodular skin lesions occur, resulting in the typical leonine (lion-like) facies § Patients often develop erythema nodosum leprosy after the onset of therapy * The incubation period averages several years, and the onset of the disease is gradual * In lepromatous leprosy, the bacilli are easily demonstrated by performing an acid-fast stain of skin lesions or nasal scrapings * In the tuberculoid form, very few organisms can be seen, and the appearance of typical granulomas is sufficient for diagnosis * The mainstay of therapy is dapsone, but because sufficient resistance to the drug has emerged, combination therapy is now recommended - Tuberculoid leprosy is treated with dapsone and rifampin for 6-12 months - Lepromatous leprosy is treated with dapsone, rifampin, and clofazimine for 12-24 months Atypical mycobacteriae Several species of mycobacteria are characterized as atypical, because they differ in certain respects from the prototype, M. tuberculosis (e.g. they are not transmissible from human to human). They are widespread in the environment and are classified according to their rate of growth and pigment production. 1) Group I (photochromogens) –> yellow-orange pigment on light exposure - M. kansasii causes lung disease clinically resembling tuberculosis - M. marinum causes “swimming pool granuloma“, which are ulcerating lesions that occur in the skin at the site of abrasions incurred in swimming pools and aquariums 2) Group II (scotochromogens) –> yellow-orange pigment in the dark - M. scrofulaceum causes scrofula, a granulomatous cervical adenitis 3) Group III (nonchromogens) –> no pigment - M. avium-intracellulare complex is composed of two species (M. avium and M. intracellulare) and causes pulmonary disease that is clinically indistinguishable from tuberculosis, primarily in immunocompromised patients 4) Group IV (rapidly growing mycobacteria) –> no pigment - M. fortuitum-chelonae complex is composed of two similar species (M. fortuitum and M. chelonae) and rarely causes skin and soft tissue infection, mostly in immunocompromised patients and those with prosthetic hip joints and indwelling catheters - M. abscessus causes chronic lung infections, as well as infections of the skin, bone, and joints - M. smegmatis is part of the normal flora of the smegma and is not associated with human disease

Answer 44

Rickettsiae are obligate intracellular bacteria Rickettsia rickettsii and Rickettsia prowazekii * Rickettsia ricketsii cause Rocky Mountain spotted fever, a life-threatening disease that occurs primarily in the South-eastern states of the US * Rickettsia prowazekii causes epidemic typhus, also a life-threatening disease that occurs mainly in crowded, unsanitary living conditions during wartime * Rickettsiae are very short rods that are barely visible in the light microscope and stain poorly with standard Gram stain, although their cell wall resembles that of gram-negative rods * Rickettsiae (except for C. burnetii) are found in certain arthropods such as ticks, lice, fleas, and mites, and are transmitted to humans by the bite of the arthropod - The rickettsiae circulate widely in the bloodstream and primarily infect the endothelium of the blood vessel walls - R. rickettsii is transmitted by ticks (main animal reservoirs are dogs and rodents) - R. prowazekii is transmitted by the human body louse (no animal reservoir) * The typical lesion caused by these rickettsiae is a vasculitis that results in the characteristic rash, edema, and hemorrhage * Rocky Mountain spotted fever is characterized by the acute onset of non-specific symptoms (e.g. fever, severe headache, myalgias, prostration) - The typical rash, which appears 2-6 days later, begins with macules that frequently progress to petechiae - The rash usually appears first on the hands and feet and then moves inward to the trunk - DIC, edema, and circulatory collapse may ensue in severe cases - It can be fatal if untreated, but diagnosed and treated cases usually cure promptly * Epidemic typhus (and other forms of typhus) begins with the sudden onset of chills, fever, headache, and other influenza-like symptoms, ~1-3 weeks after the louse bite occurs - A maculopapular rash then begins to appear on the trunk and spreads peripherally - The rash becomes petechial and spreads over the entire body, but spares the face, palms and soles - Signs of severe meningoencephalitis, including delirium and coma, begin with the rash and continue into the 2nd and 3rd weeks - In untreated cases, death occurs from peripheral vascular collapse or from bacterial pneumonia - A recurrent form of epidemic typhus is called Brill-Zinsser disease § The signs and symptoms are similar to those of epidemic typhus, but are less severe, of shorter duration, and rarely fatal § Recurrences can appear as long as 50 years later * Laboratory diagnosis of rickettsial disease is based on serologic analysis (ELISA is most often used) * The treatment of choice for all rickettsial diseases is doxycycline Other rickettsiae * R. typhi causes endemic typhus worldwide - Flea vector, rodent reservoir, symptoms similar to epidemic typhus but milder, <1% of cases are fatal * R. tsutsugamushi causes scrub typhus in Asia and Australia - Mite vector, rodent reservoir, similar to epidemic typhus, produces an eschar * R. akari causes rickettsial pox in NA, South Africa, and Korea - Mite vector, mouse reservoir, chickenpox-like illness Coxiella burnetii * Coxiella burnetii causes Q fever * C. burnetii has a spore-like stage that is highly resistant to drying, and it also has a very low infectious dose (approx. 1 organism) * The organism exists in two phases; phase 1, which is virulent, and phase 2, which is avirulent - Phase II antigen is the first to be detectable during acute Q fever, whereas high levels of phase I antibodies are detected during chronic Q fever * C. burnetii is transmitted by aerosol and inhaled into the lungs * The important reservoirs for human infection are cattle, sheep, and goats * Q fever begins suddenly with fever, severe headache, cough, and other influenza-like symptoms - Pneumonia ensues in ~50% of patients, and hepatitis may also occur - A rash is rare - The disease is usually acute, but rarely chronic Q fever characterized by life-threatening endocarditis occurs * Serologic tests are used for diagnosis * The treatment of choice is doxycycline * Persons at high risk should receive the killed vaccine for C. burnetii

Answer 45

Chlamydia trachomatis, C. pneumoniae, C. psittacci Chlamydiae are obligate intracellular bacteria. They have a rigid cell wall that resemble those of gram-negative bacteria but lack muramic acid. Chlamydiae have a unique replicative cycle that begins with the extracellular elementary body that enters the cell and reorganizes into a larger, metabolically active reticulate body. Chlamydiae infect primarily epithelial cells of the mucous membranes or the lungs. Chlamydia trachomatis * Chlamydia trachomatis causes eye (conjunctivitis, trachoma), respiratory (pneumonia), and genital tract (urethritis, lymphogranuloma venereum) infections - Infection is also associated with Reiter‘s syndrome (urethritis, arthritis, uveitis) * It is the most common bacterial cause of STDs in the US * C. trachomatis infects only humans and is usually transmitted by close personal contact (e.g. sexually or by passage through the birth canal) - In trachoma, C. trachomatis is transmitted by finger-to-eye or fomite-to-eye contact * The organism has more than 15 immunotypes (A-L) - Types A, B, and C cause trachoma, a chronic conjunctivitis endemic in Africa and Asia § Trachoma is a leading cause of blindness where it is endemic - Types D-K cause genital tract infections (e.g. urethritis, prostatitis, cervicitis, salpingitis, PID) as well as neonatal conjunctivitis and pneumonia - Types L1-L3 cause lymphogranuloma venerum, an STD with lesions on genitalia and in lymph nodes * Nucleic acid amplification tests (NAATs) using the patient‘s urine are widely used to diagnose chlamydial STD * All chlamydiae are susceptible to tetracyclines (e.g. doxycycline) and macrolides (e.g. erythromycin, azithromycin) Chlamydia pneumoniae * Chlamydia pneumoniae causes atypical pneumonia * It infects only humans and is transmitted from person to person by aerosol * Infection occurs in the upper and lower respiratory tract and is characterized by bronchitis and atypical pneumonia, mostly in young adults * Serologic tests are used to diagnose infections by C. pneumoniae and C. psittaci Chlamydia psittaci * Chlamydia psittaci causes psittacosis, a disease characterized mainly by pneumonia * It infects birds and many mammals, including humans - Humans are infected primarily by inhaling organisms in airborne dry bird feces * C. psittaci infects the lungs primarily - The infection may be asymptomatic or may produce high fever and pneumonia - Some infections can become quite severe and involve organs other than the lungs, such as the liver (hepatomegaly, jaundice), heart (myocarditis, pericarditis), and nervous system (hearing loss, transverse myelitis, and encephalitis)

Answer 46

Mycoplasmas are a group of very small, wall-less organisms, of which Mycoplasma pneumoniae is the major pathogen. They stain poorly with Gram stain and their membrane is the only bacterial membrane that contains cholesterol. Mycoplasma pneumoniae * Mycoplasma pneumoniae causes atypical pneumonia * M. pneumoniae is a pathogen only for humans and is transmitted by respiratory droplets * The organism does not invade the respiratory mucosa, but ciliary motion is inhibited and necrosis of the epithelium occurs * The mechanism by which M. pneumoniae causes inflammation is uncertain, although it is known that it produces hydrogen peroxide * During infection, autoantibodies are produced against RBCs (cold agglutinins) and brain, lung, and liver cells - These antibodies may be involved in some of the extrapulmonary manifestations of infection * M. pneumoniae infections occur worldwide, with an increased incidence in winter * This organism is the most common cause of atypical pneumonia and the most common cause of pneumonia in young adults - The term atypical means that a causative bacterium cannot be isolated on routine media in the diagnostic laboratory or that the disease does not resemble pneumococcal pneumonia * The onset of Mycoplasma pneumonia is gradual, usually beginning with a non-productive cough, sore throat, or earache - Small amounts of whitish, non-bloody sputum are produced - Constitutional symptoms of fever, headache, malaise, and myalgias are pronounced - The X-ray findings of a prominent patchy infiltrates are often in marked contrast to the paucity of findings on chest examination - The disease usually resolves spontaneously in 10-14 days * The extrapulmonary manifestations include Stevens-Johnson syndrome, erythema multiforme, Raynaud‘s phenomenon, cardiac arrhythmias, arthralgias, hemolytic anemia, and Guillan-Barré syndrome * Diagnosis can be done with a PCR assay of the sputum or respiratory secretion - Serologic testing may also be useful * The treatment of choice is either a macrolide (e.g. erythromycine, azithromycin) or a tetracycline (e.g. doxycycline) Other mycoplasmas * Mycoplasma hominis has been implicated as an infrequent cause of PID * Ureaplasma urealyticum may cause ~20% of cases of non-gonococcal urethritis - Ureaplasmas can be distinguished from mycoplasmas by their ability to produce the enzyme urease

Answer 47

Viruses are non-cellular, obligately intracellular parasites that carry infectious genetic information and have a very characteristic intracellular life cycle. Structure of viruses Viruses are composed of an internal core containing either DNA or RNA covered by a protective protein coat. Some viruses have an outer lipoprotein membrane, called an envelope, external to the coat. Viruses do not have a nucleus, cytoplasm, mitochondria or ribosomes. 1) Size and shape - Viruses range from 20-300 nm in diameter - The shape of virus particles is determined by the arrangement of repeating subunits that form the protein coat (capsid) of the virus 2) Nucleic acids - DNA or RNA, single-stranded or double-stranded, linear or circular - RNA can be either segmented or non-segmented and can have either a positive (+) or a negative (–) orientation 3) Capsid and symmetry - The capsid is made up of subunits called capsomers - Capsid + nucleic acid genome = nucleocapsid - Viral nucleocapsids have two forms of symmetry: (1) icosahedral, in which the capsomers are arranged in 20 triangles that form a spherical symmetric figure; and (2) helical, in which the capsomers are arranged in a hollow coil that appears rod-shaped § All human viruses that have a helical nucleocapsid are enclosed by an envelope 4) Envelope - Lipoprotein membrane composed of lipid derived from the host cell membrane (cytoplasmic or nuclear) and protein that is virus-specific - Present or absent depending on virus family - Enveloped viruses are more sensitive to heat, drying, detergents, and lipid solvents such as alcohol and ether Classification of viruses Virus classification can be based on the type of nucleic acid, size and symmetry of the nucleocapsid, presence of envelope, genome organization and relatedness, antigenic properties, and biological properties. Based on the first two parameters, we can classify viruses as follows: 1) DNA virus families - Parvoviridae, papillomaviridae, polyomaviridae, adenoviridae, hepadnaviridae, herpesviridae, poxviridae 2) RNA virus families with icosahedral symmetry - Picornaviridae, caliciviridae, reoviridae, flaviviridae, togaviridae, retroviridae 3) RNA virus families with helical symmetry - Orthomyxoviridae, paramyxoviridae, rhabdoviridae, filoviridae, coronaviridae, arenaviridae, bunyaviridae

Answer 48

Stages of replication 1) Adsorption (attachment) - Proteins on the surface of the virion attach to specific receptor proteins on the cell surface through weak, noncovalent bonding - The specificity of attachment determines the host range of the virus as well as the organ specificity 2) Penetration - Usually occurs shortly after adsorption and is generally an energy-dependent process - Three main mechanisms are involved i. Translocation § Entire virus particle is translocated across the cytoplasmic membrane § Relatively rare and poorly understood ii. Endocytosis § Most common mechanism § Does not require any specific virus proteins iii. Fusion § Only in enveloped viruses § Virus envelope fuses with the cytoplasmic membrane, either directly at the cell surface or in a cytoplasmic vesicle § Requires the presence of specific fusion proteins in the virus envelope (e.g. influenza hemagglutinin) 3) Uncoating - The virus capsid is completely or partially removed and the virus genome is exposed, usually in the form of a nucleoprotein complex - May occur simultaneously with penetration (as in membrane fusion) 4) Viral nucleic acid replication and expression a) DNA viruses - With the exception of poxviruses, transcription and replication occur in the nucleus and translation occurs in the cytoplasm - Only part of the genome is transcribed into early mRNA for most DNA viruses - Synthesis of “early“ or regulatory proteins is the key initial step - The remainder of the genome is transcribed into late mRNA encoding “late“ or structural proteins - Certain DNA viruses encode their own DNA polymerases, whereas others use the cellular DNA polymerases (papillomaviruses) b) RNA viruses - With the exception of influenza viruses and retroviruses, transcription and replication take place in the cytoplasm - Virus encoded RNA polymerases are needed - Replication consists of building a complementary to the viral strand of the same length, which then serves as the template for progeny viral genomes - Some viruses carry the virus encoded RNA polymerases within the virions, while others synthesize them in the infected cells 5) Maturation and release a) Naked icosahedral viruses - Pre-assembled capsomers are joined to form empty capsids (procapsids), which are the precursors of virions - The viral genome is encapsidated - Release is accompanied usually by death and lysis of the infected cell b) Enveloped viruses - Viral proteins are first associated with the nucleic acid to form the nucleocapsid - Nucleocapsid is then surrounded by an envelope, usually via the process of budding through the outer cell membrane § Herpesviruses are the exception to this, since they acquire their envelopes from the nuclear membrane - The carbohydrates and lipids in the envelope are produced by the host cell

Answer 49

The stages of viral pathogenesis are the following: 1) Virus entry / primary replication 2) Viral spread 3) Cell injury 4) Virus shedding Portals of entry * Skin - Injury (papillomavirus, HSV), animal bite (rabies virus), vector transmission (yellow fever virus), contaminated needle injection (HBV, HIV) * Respiratory tract (aerosol) - Can cause local infection (influenza virus) or systemic infection (measles virus, mumps virus) * Gastrointestinal tract (fecal-oral transmission) - Can cause local infection (rotavirus) or systemic infection (HAV) * Urogenital tract (usually sexual transmission) - Can cause local infection (HSV2, HPV) or systemic infection (HIV, HBV) * Conjunctiva - Certain adenoviruses and enteroviruses Localized and disseminated infections * Most viral infections are either localized to the portal of entry or spread systemically through the body * The best example of the localized infection is the common cold caused by rhinoviruses, which involves only the upper respiratory tract * One of the best-understood systemic viral infections is paralytic poliomyelitis - After poliovirus is ingested, it infects and multiplies within the cells of the small intestine and then spreads to the mesenteric lymph nodes, where it multiplies again and can then enter the bloodstream to spread to certain internal organs * Viruses that spread systemically may do so via the bloodstream or by retrograde axonal flow within neurons (e.g. rabies virus) Mechanisms of cell injury a) Direct cytopathic effect (CPE) - Probably due to inhibition of macromolecular (protein, DNA, RNA) synthesis - Usually begins with rounding and darkening of the cell and culminates in either lysis (disintegration) or giant cell formation (fusion of virus-infected cells) b) Injury by the immune response - Both cytotoxic T cells and antibodies play a role in the immunopathogenesis - Also occurs when virus-antibody-complement complexes form and are deposited in various tissues (e.g. in hepatitis B) c) Alteration of cell function - An example of this is the rotavirus, which induces its host cell (enterocytes) to produce cytokines that stimulate the enteric nervous system, resulting in excess fluid and electrolyte secretion into the bowel lumen

Answer 50

Cultivation * Viruses require cell cultures for growth because they replicate only in living cells * Virus growth in cell culture frequently produces a characteristic cytopathic effect (CPE) that can provide a presumptive identification - CPE is a change in the appearance of the virus-infected cells (see topic #3, “Mechanisms of cell injury“) * If the virus does not produce a CPE, the presence can be detected by several other techniques a) Hemadsorption – attachment of RBCs to the surface of virus-infected cells, limited to viruses with a hemagglutinin protein on their envelope (e.g. mumps, influenza) b) Interference – by adding another virus that does produce a CPE, we can detect the presence of one that doesn‘t through its interference (e.g. detection of rubella virus with certain enteroviruses) c) Decrease in acid production – infected and dying cells decrease their acid production, which can be detected by a color change in the phenol red (a pH indicator) in the culture medium Nucleic acid detection * Viral nucleic acids (either the viral genome or viral mRNA) can be detected in the patient‘s blood or tissues with complementary DNA or RNA (cDNA or cRNA) as a probe * PCR can be used to amplify the viral nucleic acids if only a small amount is present * Assays for the RNA of HIV and HCV and the DNA of HBV in the patient‘s blood are commonly used to monitor the course of the disease and to evaluate the patient‘s prognosis Antigen detection * Viral antigens can be detected in the patient‘s blood or body fluids by various tests, but most often by ELISA * Tests for the p24 antigen of HIV and the surface antigen of HBV are common examples of this approach Electron microscopy * Electron microscopy can be used on clinical specimens such as biopsy material or skin lesions to detect virus particles, which can be characterized by their size and morphology Serological methods * A rise in the titer of antibody to the virus can be used to diagnose current infection * Seroconversion is the term used to describe the finding of an antibody to a virus (or any microbe) in a patient‘s serum when the patient previously had no antibody * A serum sample is obtained as soon as a viral etiology is suspected (acute-phase), and a second sample is obtained 10-14 days later (convalescent-phase) - If the antibody titer in the convalescent-phase serum sample is at least 4x higher than the titer in the acute-phase serum sample, the patient is considered to be infected * An antibody titer on a single sample does not distinguish between a previous infection and a current one * Several serological methods are currently in routine use for virus detection 1) Complement fixation - If the antigen (the unknown virus) and the known antibody are a match, complement will be fixed to the antigen-antibody complex and will be unavailable to lyse the “indicator“ system (sensitized RBCs) 2) Hemagglutination inhibition - If the virus and the antibody are a match, the virus is blocked from attaching to the RBCs and no hemagglutination occurs 3) Neutralization - If the virus and the antibody are a match, the antibody bound to the surface of the virus blocks its entry into the cell and prevents subsequent CPE formation 4) Fluorescent antibody assay - If the virus-infected cells and the fluorescein-tagged antibody are a match, the typical apple-green color of fluorescein is seen in the cells by UV microscopy 5) Radioimmunoassay - If the virus and the antibody are a match, there is less antibody remaining to bind the known radiolabeled virus 6) ELISA - Known antibody is bound to a surface and if the virus is present it will bind to the antibody - A sample of the antibody linked to an enzyme is then added, which will attach to the bound virus and, upon addition of substrate to the enzyme, the amount of bound enzyme can be determined 7) Immunoelectron microscopy - If the virus and the antibody are a match, aggregates of virus-antibody complexes are seen in the electron microscope

Answer 51

Some details about viral vaccines can also be found in topic #13 of the first (I) part. Since the title of that topic does not discriminate between bacterial and viral vaccines I thought it best to include information about both. There are three types of vaccines that induce active immunity 1) Attenuated live-virus vaccines - MMR (measles, mumps, rubella), sabin (oral polio vaccine), 17 D vaccine (yellow fever), rotavirus vaccine - Preferred to killed or subunit vaccines because their protection is greater and longer-lasting - Produces a strong IgG response, and can also produce a strong IgA response when administered by the natural route of infection (e.g. polio vaccine given orally) - Can revert to virulence either during vaccine production or in the immunized person § Of the commonly used live-virus vaccines, only polio vaccine has had problems regarding revertants - Can be excreted by the immunized person, which is advantageous in the sense that it can therefore successfully immunize others, but could also be a problem if a virulent revertant spreads to a susceptible person - A second virus could contaminate the vaccine if it was present in the cell cultures used to prepare the vaccine 2) Killed-virus vaccines - Salk vaccine (inactivated polio vaccine), rabies vaccine, hepatitis A vaccine - Induce a shorter duration of protection and are less protective - Usually given intramuscularly and therefore do not stimulate a major IgA response - Virus does not replicate so cytotoxic T-cell response is not elicited - Cannot revert to virulence and are more heat-stable - Can also be contaminated by a second virus, but it is less likely 3) Subunit vaccines - Hepatitis B vaccine (composed of purified HBsAg), HPV vaccines - Features resemble those of killed vaccines because no viral replication occurs

Answer 52

Inhibition of early events a) Amantadine blocks the replication of influenza A virus by inhibiting the uncoating of the virus b) Enfuvirtide binds to gp41 on the surface of HIV, thereby blocking its entry into the cell c) Maraviroc blocks the binding of HIV to CCR-5, an important coreceptor for those strains of HIV that use CCR-5 for entry into the cell d) Palivizumab is a monoclonal antibody that neutralizes respiratory syncytial virus (RSV) by binding to the fusion protein on the virus‘ surface Inhibition of viral nucleic acid synthesis I. Inhibitors of herpesviruses a) Acyclovir is a guanosine analogue that inhibits viral DNA polymerase after phosphorylation by the virus-encoded thymidine kinase - Primarily effective against HSV-1, HSV-2, and VZV b) Ganciclovir is structurally similar to acyclovir but is more active against CMV - Activated by a CMV-encoded phosphokinase in a similar process to acyclovir c) Cidofovir is a cytosine analogue that does not have to be phosphorylated to be effective d) Foscarnet is a pyrophosphate analogue that binds to DNA polymerase and inhibits extension of the DNA strand - Effective against all herpesviruses, especially HSV and CMV e) Valacyclovir is a derivative of acyclovir f) Valganciclovir is a derivative of ganciclovir II. Inhibitors of retroviruses a) Abacavir is a guanosine analogue that causes chain termination during DNA synthesis b) Lamivudine is a nucleoside analogue that causes chain termination during DNA synthesis c) Tenofovir is an AMP analogue that causes chain termination during DNA synthesis d) Zidovudine is a nucleoside analogue that causes chain termination during DNA synthesis e) Efavirenz binds near the active side of the reverse transcriptase and induces a conformational change that inhibits the synthesis of viral DNA - Effective in combination with zidovudine plus lamivudine III. Inhibitors of HBV a) Entecavir is a guanosine analogue that inhibits the DNA polymerase (reverse transcriptase) of HBV b) Lamivudine – described above c) Tenofovir – described above IV. Inhibitors of HCV a) Sofosbuvir (NS5B inhibitor)is a uridine analogue that inhibits the RNA polymerase of HCV and causes chain termination b) Velpatasvir inhibits NS5A, an RNA-binding protein required for the activity of the RNA polymerase of HCV - Available in combination with sofosbuvir V. Inhibitors of other viruses a) Ribavirin is a nucleoside analogue that inhibits the synthesis of guanine nucleotides - Used to treat pneumonitis caused by RSV in infants and to treat severe influenza B infections Inhibition of integrase a) Raltegravir blocks the HIV-encoded integrase that mediates the integration of newly synthesized viral DNA into the host cell DNA Inhibition of protease I. Inhibitors of HIV a) Ritonavir inhibits the protease encoded by HIV and prevents the production of several nucleocapsid and enzymatic proteins - Typically used in combination with another protease inhibitor II. Inhibitors of HCV a) Grazoprevir inhibits a serine protease required for the replication of HCV Inhibition of viral protein synthesis a) Fomivirsen is an anti-sense DNA strand that blocks the replication of CMV by binding to viral mRNA b) Interferon-α binds to a receptor on the cell surface that signals the cell to synthesize three proteins that cause both viral and cellular protein synthesis to be inhibited - Approved for use in patients with chronic hepatits B and C Inhibition of release of virus a) Oseltamivir inhibits the neuraminidase of influenza virus, thereby blocking its release from the infected cell Antiviral defense a) Imiquimod stimulates toll-like receptor 7 (TLR7), leading to the secretion of various cytokines (INF-α, IL-6, TNF-α) that improve host defenses - Used to treat genital warts, superficial basal cell carcinoma, and actinic keratosis

Answer 53

* Adenoviruses cause a variety of upper and lower respiratory tract diseases such as pharyngitis, conjunctivitis, the common cold, and pneumonia - Keratoconjunctivitis, hemorrhagic cystitis, and gastroenteritis also occur * Adenoviruses are non-enveloped viruses with double-stranded linear DNA and an icosahedral nucleocapsid - Protruding from each of the 12 vertices of the capsid is a fiber that acts as the organ of attachment and is a hemagglutinin * After attachment to the cell surface via its fiber, the virus penetrates and uncoats, and the viral DNA moves to the nucleus - Host cell DNA-dependent RNA polymerase transcribes the early genes, and after viral DNA replication late mRNA is transcribed - Viral assembly occurs in the nucleus, and the virus is released by lysis of the cell * Adenoviruses can be transmitted with respiratory droplets, via the fecal-oral route, or by direct inoculation of the conjunctivas * Adenovirus infections are endemic worldwide, but outbreaks occur in close living conditions that facilitate transmission (e.g. military camps) * Certain serotypes are associated with specific syndromes (e.g. types 3,4,7, and 21 cause respiratory disease whereas types 40 and 41 cause infantile gastroenteritis) * In the upper respiratory tract, adenoviruses cause infections such as pharyngitis, pharyngoconjunctival fever, and acute respiratory disease (fever, sore throat, runny nose, conjunctivitis) * In the lower respiratory tract, they cause bronchitis and atypical pneumonia * In the urogenital tract, they cause hemorrhagic cystitis, characterized by hematuria and dysuria * In the GI tract, they cause non-bloody diarrhea, mainly in children younger than 2 years of age * Most infections resolve spontaneously and ~50% of all infections are asymptomatic * Diagnosis is based on isolation of the virus in cell culture and a rise in antibody titer * There is no antiviral therapy * Three, live, non-attenuated vaccines against serotypes 4, 7, and 21 are available but are used only by the military

Answer 54

Herpes simplex viruses (HSV) * Herpes simplex viruses are enveloped viruses with double-stranded linear DNA and an icosahedral nucleocapsid * HSV-1 causes acute gingivostomatitis, recurrent herpes labialis (cold sores), keratoconjunctivitis (keratitis), and encephalitis, primarily in adults * HSV-2 causes herpes genitalis (genital herpes), neonatal encephalitis and other forms of neonatal herpes, and aseptic meningitis * Infection by HSV-1 or HSV-2 is a common cause of erythema multiforme * HSV-1 and HSV-2 are structurally and morphologically indistinguishable, but have different antigenicity and cause lesions in different locations * Humans are the natural hosts of both HSV-1 and HSV-2 * The replicative cycle begins when HSV-1 binds first to heparan sulfate on the cell surface and then to a second receptor, nectin - Fusion occurs and the nucleocapsid and tegument proteins are released into the cytoplasm - The viral nucleocapsid is transported to the nucleus where the linear DNA genome becomes circular - Early genes are transcribed by the host cell RNA polymerase, and then the viral DNA polymerase replicates the genome DNA at the same time as late genes are transcribed - Virions are assembled in the nucleus and then obtain their envelope by budding through the nuclear membrane before exiting the cell via tubules or vacuoles * HSV-1 is transmitted primarily in saliva, whereas HSV-2 is transmitted by sexual contact * The virus replicates in the skin or mucous membrane at the initial site of infection, and then migrates up the neuron by retrograde axonal flow and becomes latent in the sensory ganglion cells - In general, HSV-1 becomes latent in the trigeminal ganglia, whereas HSV-2 becomes latent in the lumbar and sacral ganglia - Most, if not all, of the viral DNA is located in the cytoplasm during latency * The typical lesion is a vesicle that contains serous fluid filled with cell debris and virus particles that can be spread to other individuals upon rupture of the vesicle * HSV-1 causes several forms of primary and recurrent disease - Gingivostomatitis occurs primarily in children and is characterized by fever, irritability, and vesicular lesions in the mouth - Herpes labialis (fever blisters or cold sores) is the milder, recurrent form and is characterized by crops of vesicles, usually at the mucocutaneous junction of the lips or nose - Keratoconjunctivitis is characterized by corneal ulcers and lesions of the conjunctival epithelium - Encephalitis caused by HSV-1 is characterized by a necrotic lesion in one temporal lobe, which is accompanied by fever, headache, vomiting, seizures, and altered mental status - Herpetic whitlow is a pustular lesion of the skin of the finger or hand - Herpes gladiatorum is characterized by vesicular lesions on the head, neck, and trunk and primarily occurs in wrestlers - Eczema herpeticum is an infection of the skin of a patient with atopic dermatitis - Disseminated infections, such as esophagitis and pneumonia, occur in immunocompromised patients * HSV-2 causes several diseases, both primary and recurrent - Genital herpes is characterized by painful vesicular lesions of the male and female genitals and anal area - Neonatal herpes originates chiefly from contact with vesicular lesions within the birth canal and can vary from severe disease (e.g. disseminated lesions or encephalitis) to milder local lesions (skin, eye, mouth) to asymptomatic infection - Aseptic meningitis caused by HSV-2 is usually a mild, self-limited disease with few symptoms * A rapid presumptive diagnosis can be made from skin lesions by using the Tzanck smear, in which cells from the base of the vesicle are stained with Giemsa stain - The presence of multinucleated giant cells suggests herpesvirus infection * PCR assay can be done if herpes encephalitis is suspected * Acyclovir is the treatment of choice for encephalitis and systemic disease caused by HSV-1 - It is also useful for the treatment of primary and recurrent genital herpes, neonatal herpes, and keratitis * Valacyclovir and famciclovir are used in the treatment of genital herpes and in the suppression of recurrences Varicella-zoster virus (VZV) * Varicella (chickenpox) is the primary disease; zoster (shingles) is the recurrent form * VZV is structurally and morphologically similar to other herpesviruses but is antigenically different * The replicative cycle is similar to that of HSV The virus is transmitted by respiratory droplets and by direct contact with the lesions * Varicella occurs worldwide and is a highly contagious disease of childhood * VZV infects the mucosa of the upper respiratory tract and then spreads via the blood to the skin, where the typical vesicular rash occurs - Multinucleated giant cells with intranuclear inclusions are seen in the base of the lesions * The virus infects sensory neurons and is carried by retrograde axonal flow into the cells of the dorsal root ganglia, where it becomes latent - VZV DNA is located in the nucleus, but is not integrated into cellular DNA * A person gets varicella only once, but zoster can occur despite immunity to varicella - Zoster usually occurs only once * In varicella after an incubation period of 14-21 days, brief prodromal symptoms of fever and malaise occur - A papulovesicular rash then appears in crops on the trunk and spreads to the head and extremities - Itching (pruritus) is a prominent symptom, especially when vesicles are present - Varicella is mild in children but more severe in adults (varicella pneumonia and encephalitis are the major rare complications) * Zoster is characterized by the occurrence of painful vesicles along the course of a sensory nerve of the head or trunk - The pain can last for weeks, and post-zoster neuralgia (a.k.a. post-herpetic neuralgia) can be debilitating - Immunocompromised patients are at risk for life-threatening disseminated infections such as pneumonia * Most diagnosis are made clinically but a presumptive diagnosis can be made in the laboratory using the Tzanck smear * No antiviral therapy is necessary for chickenpox or zoster in immunocompetent children, but adults can be treated with acyclovir - Immunocompromised patients should always be treated with acyclovir * There are two vaccines against VZV, one that is designed to prevent varicella and another designed to prevent zoster - Both contain live, attenuated VZV, but the zoster vaccine contains 14x more virus - The varicella vaccine is recommended for children between the ages of 1 and 12 years, whereas the zoster vaccine is recommended for people older than 60 years who have had varicella

Answer 55

Cytomegalovirus (CMV) • CMV causes cytomegalic inclusion disease in neonates and is the most common cause of congenital abnormalities in the US - It is an important cause of pneumonia and other diseases in immunocompromised patients - It also causes heterophil-negative mononucleosis in immunocompetent patients • CMV is structurally and morphologically similar to other herpesviruses but is antigenically different • The replicative cycle is similar to that of HSV • CMV can be transmitted across the placenta, within the birth canal, via breast milk, via saliva, sexually, during blood transfusions, and during organ transplants • CMV infection occurs worldwide and more than 80% of adults have antibody against the virus • Infection of the fetus can cause cytomegalic inclusion disease, characterized by multinucleated giant cells with prominent intramuscular inclusions - Approximately 20% of infants infected with CMV during gestation show clinically apparent manifestations such as microcephaly, seizures, deafness, jaundice, and purpura (lesions resemble a “blueberry muffin“ and are due to thrombocytopenia) - Hepatosplenomegaly is very common - One of the leading causes of mental retardation in the US • Infections of children and adults are usually asymptomatic, except in immunocompromised individuals - In immunocompetent adults, CMV can cause heterophil-negative mononucleosis, characterized by fever, lethargy, and the presence of abnormal lymphocytes in peripheral blood smears - In immunocompromised patients, systemic CMV infections (especially pneumonitis, esophagitis, and hepatitis) occur in a high proportion - CMV can also cause colitis with diarrhea and retinitis in AIDS patients • CMV enters a latent state primarily in monocytes and can be reactivated when cell-mediated immunity is decreased • The preferred approach to diagnosis involves culturing and immunofluorescence assay, which can make a diagnosis in 72 hours - Other diagnostic methods include staining of inclusion bodies (oval owl‘s eye shape) in giant cells in urine and in tissue • Ganciclovir is moderately effective in the treatment of CMV retinitis and pneumonia in patients with AIDS - Foscarnet and cidofovir can also be used Human herpesvirus 6 (HHV-6) • HHV-6 is the cause of exanthem subitum (roseola infantum), a common disease in infants that is characterized by a high fever and a transient macular or maculopapular rash • The virus is found worldwide, and up to 80% of people are seropositive • HHV-6 infects T- and B-cells and remain latent within them, but can be reactivated in immunocompromised patients and cause pneumonia • Many virologic and clinical features of HHV-6 are similar to CMV

Answer 56

Epstein-Barr virus (EBV) • EBV causes infectious mononucleosis - It is associated with Burkitt‘s lymphoma, other B-cell lymphomas, and nasopharyngeal carcinoma - EBV also causes hairy leukoplakia • EBV is structurally and morphologically similar to other herpesviruses but is antigenically different - The most important antigen of EBV is viral capsid antigen (VCA), because it is used most often in diagnostic tests • EBV infects mainly lymphoid cells, primarily B lymphocytes, but it also infects epithelial cells of the pharynx, resulting in prominent sore throat • In latently infected cells, EBV DNA is in the nucleus and is not integrated into the cellular DNA • The replicative cycle is similar to that of HSV • EBV is transmitted primarily by the exchange of saliva (e.g. during kissing) and is one of the most common infections worldwide (>90% of adults in the US are seropositive) • The infection occurs first in the oropharynx and then spreads to the blood, where it infects B lymphocytes - Specific antibodies against the viral capsid antigen as well as non-specific heterophil antibodies are produced against EBV • Infectious mononucleosis is characterized primarily by fever, sore throat, lymphadenopathy, and splenomegaly - Anorexia and lethargy are prominent, hepatitis is frequent, and encephalitis occurs in some patients - Spontaneous recovery usually occurs in 2-3 weeks • EBV also causes a severe, often fatal, progressive form of infectious mononucleosis in children with an inherited immunodeficiency called X-linked lymphoproliferative syndrome (75% mortality by age 10) • Hairy leukoplakia is a whitish, non-malignant lesion with an irregular “hairy“ surface on the lateral side of the tongue seen in immunocompromised individuals with EBV infection • EBV infection can be detected with serologic tests targeting specific and non-specific antibodies • No antiviral therapy is necessary for uncomplicated infectious mononucleosis, but administration of high doses of acyclovir may be useful in life-threatening cases Human herpesvirus 8 (HHV-8) • HHV-8 causes Kaposi‘s sarcoma (KS), the most common cancer in patients with AIDS • HHV-8 causes malignant transformation by a mechanism similar to that of other DNA viruses (e.g. HPV), namely, inactivation of a tumor suppressor gene (RB and p53) • Transmission of HHV-8 occurs primarily via sex and by saliva, but is also transmitted in transplanted organs such as kidneys • KS in AIDS patients is a malignancy of vascular endothelial cells - It manifests as reddish to dark purple, flat to nodular lesions that often appear at multiple sites such as the skin, oral cavity, and soles (but not the palms) - Internally, lesions occur commonly in the GI tract and the lungs • HHV-8 also infects B-cells, inducing them to proliferate and produce a type of lymphoma called primary effusion lymphoma • Surgical excision, radiation, chemotherapy, or immunomodulatory drugs can be used for treatment of KS

Answer 57

• Parvovirus B19 causes erythema infectiosum (slapped cheek syndrome, fifth disease), aplastic anemia (especially in patients with sickle cell anemia), and fetal infections, including hydrops fetalis • Parvovirus B19 is a very small (22 nm) non-enveloped virus with a single-stranded DNA genome (negative-strand) and an icosahedral nucleocapsid • After adsorption to host cell receptors, the virion penetrates and moves into the nucleus, where replication occurs - Cellular DNA polymerase initiates the synthesis of the progeny genomes and the viral mRNA is synthesized by cellular RNA polymerase from the double-stranded DNA intermediate - The progeny virions are assembled in the nucleus • B19 virus is transmitted primarily by the respiratory route, although transplacental and transfusion-related transmission also occurs • B19 virus infection occurs worldwide and humans are the natural reservoir • The virus primarily infects erythroblasts in the bone marrow and endothelial cells in the blood vessels - In addition to the direct cytopathic effect of the virus, immune complexes composed of the virus and IgM or IgG also contribute to the pathogenesis of erythema infectiosum and arthritis that is seen in some infected adults • Erythema infectiosum (slapped cheek syndrome, fifth disease) is a mild disease, primarily of childhood, characterized by a bright red rash that is most prominent on the cheeks, accompanied by low-grade fever, runny nose, and sore throat - Symptoms resolve in ~1 week • Transient but severe aplastic anemia (aplastic crisis) usually only occurs in individuals with chronic anemia, such as sickle cell anemia, thalassemia, and spherocytosis • If a woman is infected with B19 virus during the first or second trimester of pregnancy, the virus may cross the placenta and infect the fetus - Infection during the first trimester results in fetal death, whereas infection during the second trimester leads to hydrops fetalis as a result of congestive heart failure • Parvovirus B19 infection in adults, especially women, can cause arthritis mainly involving the small joints of the hands and feet bilaterally • Chronic B19 infection can cause chronic anemia, leukopenia, or thrombocytopenia in people with immunodeficiencies • Diagnosis is made with serologic tests or PCR assays • There is no specific treatment of B19 infection Smallpox virus • Smallpox virus, also called variola virus, is the agent of smallpox, the only human disease that has been eradicated from the face of the Earth • Poxviruses are brick-shaped particles containing linear double-stranded DNA, a disk-shaped core within a double membrane, and a lipoprotein envelope • After penetration of the cell and uncoating, the virion DNA-dependent RNA polymerase synthesizes early mRNA - The viral DNA is then replicated, after which late genes are transcribed to form progeny virions - The virions are assembled in the cytoplasm and acquire their envelopes by budding from the cell membranes as they are released from the cell • Smallpox virus is transmitted via respiratory aerosol or by direct contact with the virus either in the skin lesions or on fomites such as bedding • Smallpox begins when the virus infects the upper respiratory tract and local lymph nodes and then enters the blood (primary viremia) - Internal organs are infected, and then the virus re-enters the blood (secondary viremia) and spreads to the skin • After an incubation period of 7-14 days, there is a sudden onset of prodromal symptoms such as fever and malaise - This is followed by the rash, which is worse on the face and extremities than on the trunk - The rash evolves through stages from macules to papules, vesicles, pustules, and finally crusts in 2-3 weeks • The disease was eradicated by global use of the smallpox vaccine, which contains live, attenuated vaccinia virus (another poxvirus that is less likely to cause human disease) Molluscum contagiosum virus • Molluscum contagiosum virus (MCV) is a member of the poxvirus family but is quite distinct from smallpox and vaccinia viruses • The lesion of molluscum contagiosum is a small (2-5 mm), flesh-colored papule on the skin or mucous membrane that is painless, non-pruritic, and not inflamed - The lesions have a characteristic cup-shaped (umbilicated) crater with a white core and is composed of hyperplastic epithelial cells with cytoplasmic inclusion bodies • MCV is transmitted by close personal contact, including sexually • The disease is quite common in children, in whom lesions often occur around the eyes and on the trunk • Diagnosis is typically made clinically and removal of the lesions by curettage or with liquid nitrogen is typically the only treatment

Answer 58

Orthomyxoviridae (Influenza A, B, C) * Influenza A virus causes worldwide epidemics (pandemics) of influenza, influenza B virus causes major outbreaks of influenza, and influenza C virus causes mild respiratory tract infections but does not cause outbreaks - Pandemics occur when a variant of IAV with a new hemagglutinin against which people do not have pre-existing antibodies is introduced into the human population * Influenza virus is composed of a segmented single-stranded RNA genome, a helical nucleocapsid, and an outer lipoprotein envelope - The virion contains an RNA-dependent RNA polymerase, which transcribes the negative-strand genome into mRNA - The envelope is covered with two different types of spikes, a hemagglutinin (HA) and a neuraminidase (NA) § HA binds to the sialic acid receptor and initiates infection of the cell § NA cleaves sialic acid to release the progeny virus from the infected cell * There are two types of antigenic changes involving HA and NA, based on reassortment of segments of the genome RNA a) Antigenic drift (IAV and IBV) - Minor change based on mutations in the RNA genome b) Antigenic shift (only IAV) - Major change based on the reassortment of segments of the RNA genome - Animal influenza A viruses are the source of the new RNA segments * The internal ribonucleoprotein in the nucleocapsid is the group-specific antigen that distinguishes influenza A, B, and C viruses, whereas HA and NA are the type-specific antigens - In humans, three types of HA (H1, H2, and H3) and two type of NA (N1 and N2) predominate * After adsorbing to the cell surface, the virus enters the cell in vesicles and uncoats within an endosome - The nucleocapsid then migrates to the nucleus where the RNA genome is transcribed - Most of the transcribed mRNA moves to the cytoplasm, where it is translated into viral proteins, while some remains in the nucleus to serve as a template for the synthesis of the negative-strand RNA genomes for the progeny virions - The helical ribonucleoprotein assembles in the cytoplasm, matrix protein mediates the interaction of the nucleocapsid with the envelope, and the virion is released from the cell by budding from the outer cell membrane * The virus is transmitted by airborne respiratory droplets * Infections occur primarily in the winter months of December to February in the northern hemisphere, and in the winter months of June through August in the southern hemisphere * Influenza virus infection causes inflammation of the mucosa of the upper respiratory tract sites such as the nose and pharynx, and lower respiratory tract sites such as the larynx, trachea, bronchi, and alveoli (pneumonia) - After an incubation period of 24-48 hours, fever, myalgias, headache, sore throat, and cough develop suddenly - Vomiting and diarrhea are rare symptoms - Systemic symptoms are due to cytokines circulating in the blood - The symptoms usually resolve spontaneously in 4-7 days, but influenzal or bacterial pneumonia may complicate the course * Reye‘s syndrome, characterized by encephalopathy and liver degeneration, is a rare, life-threatening complication in children following some viral infections, particularly influenza B and chickenpox - Aspirin given during viral infection has been implicated in the pathogenesis * Although most diagnoses of influenzas are made on clinical grounds, laboratory tests are available - ELISA is most commonly used, with several rapid types available that are suitable for a physician‘s office - A rise in antibody titer, PCR, and isolation of the virus on cell culture are also useful * Oseltamivir taken orally and zanamivir inhaled into the nose are the two most commonly used drugs for the treatment of influenza - Oseltamivir is also used as prophylaxis in the elderly * Amantadine is approved for both the treatment and prevention of influenza A, but resistance has emerged rapidly (especially of H3N2 strains) * Trivalent and quadrivalent subunit vaccines are available against influenza A and B and should be given to those at risk of severe influenza infection (e.g. elderly) - A live, attenuated vaccine containing temperature-sensitive mutants of influenza A and B is also available (can replicate in nasal mucosa but not in lower resp. tract)

Answer 59

Paramyxoviridae (Measles virus, Mumps virus, RSV, Parainfluenza virus) Paramyxoviruses are single-stranded RNA (negative-sense) viruses with a helical nucleocapsid and an outer lipoprotein envelope. Parainfluenza viruses * Parainfluenza viruses causes croup (acute laryngotracheobronchitis), laryngitis, bronchiolitis, and pneumonia in children and a disease resembling the common cold in adults * The surface spikes of parainfluenza viruses consist of hemagglutinin, neuraminidase, and fusion proteins Both humans and animals are infected by parainfluenza viruses, but the animal strains do not infect humans * There are four types of parainfluenza virus, which are distinguished by antigenicity, cytopathic effect, and pathogenicity * After adsorption to the cell surface via its hemagglutinin, the virus penetrates and uncoats and the virion RNA polymerase transcribes the negative-strand genome into mRNA - After translation of the mRNA into specific viral proteins, the helical nucleocapsid is assembled, the matrix protein mediates the interaction with the envelope, and the virus is released by budding from the cell membrane * These viruses are transmitted via respiratory droplets and causes disease worldwide, primarily in the winter months * Croup is characterized by a harsh cough and hoarseness * Most infections are diagnosed clinically, and there is no antiviral therapy or vaccine Respiratory syncytial virus (RSV) * Respiratory syncytial virus (RSV) is the most important cause of pneumonia and bronchiolitis in infants - It is also an important cause of otitis media in children and of pneumonia in the elderly as well as patients with chronic cardiopulmonary diseases * The surface spikes of RSV are fusion proteins, which cause cells to fuse and form multinucleated giant cells (syncytia), which give rise to the name of the virus * There are two serotypes (subgroup A and B) and humans are the natural hosts * Replication is similar to that of parainfluenza viruses * Transmission occurs via respiratory droplets and by direct contact of contaminated hands with the nose or mouth * The virus causes outbreaks of respiratory infections every winter worldwide and virtually everyone has been infected by the age of 3 years * RSV infection in infants is more severe and more often involves the lower respiratory tract than in older children * Infections in older children and young, healthy adults cause only minor disease, such as the common cold and bronchitis * A rapid antigen test that detects RSV antigens in respiratory secretions is commonly used for diagnosis * Aerosolized ribavirin is recommended for severely ill hospitalized infants, but there is uncertainty regarding its effectiveness Coronavirus (Coronaviridae) Coronaviruses * Coronaviruses are an important cause of the common cold, probably second only to rhinoviruses in frequency * Although they usually only cause mild to moderate upper respiratory tract illnesses, three new coronaviruses have emerged from animal reservoirs over the past decades to cause serious and widespread illness and death - In 2002, an atypical pneumonia caused by a coronavirus (SARS-CoV) called severe acute respiratory syndrome (SARS) emerged - In 2012, another severe pneumonia caused by a coronavirus (MERS-CoV) called Middle East respiratory syndrome (MERS) emerged - In 2019, another severe pneumonia caused by a coronavirus (SARS-CoV-2) called COVID-19 (coronavirus infectious disease-19) emerged * Coronaviruses have a non-segmented, single-stranded, positive-polarity RNA genome, a helical nucleocapsid, and an envelope * The virus adsorbs to cells via its surface spikes (hemagglutinin), after which it enters the cytoplasm where it is uncoated - The genome is translated and the viral RNA polymerase is formed to replicate the viral genome - mRNAs are also synthesized and then translated into structural proteins - The virus is assembled and obtains its envelope from the endoplasmic reticulum - Replication occurs in the cytoplasm * Coronaviruses are transmitted by respiratory aerosol * Coronavirus infection is typically limited to the mucosal cells of the respiratory tract * The common cold caused by coronavirus is characterized by a runny nose (coryza), scratchy sore throat, and low-grade fever that typically lasts several days * There is no antiviral therapy or vaccine available for coronaviruses * SARS originated in China in November of 2002 * The MERS outbreak occurred in 2012-13 in Saudi Arabia and other countries in the region * COVID-19 originated in China in December of 2019 - Any infected person can have mild to severe symptoms, but older adults and those with severe underlying medical conditions (heart or lung disease, diabetes, malignant tumor, hypertension) have a higher risk of developing severe COVID-19 illness - Symptoms may appear 2-14 days after exposure to the virus - Characteristic symptoms of COVID-19 are dry cough, shortness of breath, fever, muscle pain, and new loss of taste or smell - Gastrointestinal symptoms (nausea, vomiting, diarrhea) can also develop - Hypoxia due to respiratory distress and a severe inflammatory reaction can lead death - As of this writing (29th of June, 2020), there have been over 10 million cases reported with over 500,000 deaths worldwide

Answer 60

* Mumps virus is a paramyxovirus that causes mumps, a disease that occurs primarily in childhood and is characterized by salivary gland swelling * The surface spikes of mumps virus are hemagglutinin and neuraminidase (single spike that has both abilities) and fusion protein * Replication is similar to that of parainfluenza viruses * Mumps virus is transmitted by respiratory droplets * Mumps occurs worldwide, with a peak incidence in the winter * The virus infects the upper respiratory tract and then spreads through the blood to infect the salivary glands, especially the parotid gland, testes, ovaries, pancreas, and, in some cases, meninges * Lifelong immunity occurs in persons who have had the disease * After an incubation period of 18-21 days, a prodromal stage of fever, malaise, and anorexia is followed by tender swelling of the salivary glands, either unilaterally or bilaterally - The disease is typically benign and resolves spontaneously within 1 week - Complications include orchitis in postpubertal males (can result in sterility if bilateral) and meningitis (usually benign, self-limited, and without symptoms) * Diagnosis of mumps is usually made clinically, but laboratory tests, such as PCR assay and a rise in antibody titer, can be used for confirmation * There is no antiviral therapy for mumps * Prevention consists of immunization with the live, attenuated vaccine, which is usually given in combination with measles and rubella vaccines (MMR vaccine)

Answer 61

* Measles virus is a paramyxovirus that causes measles, a disease that occurs primarily in childhood and is characterized by a maculopapular rash * The virion has two types of envelope spikes, a hemagglutinin and a fusion protein (cell-fusing and hemolytic activities) * The replicative cycle is similar to that of parainfluenza viruses * Measles virus is transmitted via respiratory droplets produced by coughing and sneezing both during the prodromal period and for a few days after the rash appears * Measles occur worldwide, usually in outbreaks every 2-3 years, when the number of susceptible children reaches a high level * In malnourished children, especially those in developing countries, measles is a much more serious disease than in well-nourished children * After infecting the cells lining the upper respiratory tract, the virus enters the blood and infects reticuloendothelial cells, where it replicates again - It then spreads via the blood to the skin, where a rash appears caused primarily by cytotoxic T cells attacking the virus-infected vascular endothelial cells * Lifelong immunity occurs in individuals who have had the disease * After an incubation period of 10-14 days, a prodromal phase characterized by fever, conjunctivitis, runny nose, and coughing occurs - Koplik‘s spots are bright red lesions with a white, central dot that are located on the buccal mucosa and are virtually diagnostic - A few days later, a maculopapular rash appears on the face and proceeds gradually down the body to the lower extremities, including the palms and soles - The rash develops a brownish hue several days later * The complications of measles can be quite severe - Encephalitis occurs in 1/1000 cases of measles, with a mortality rate of 10% and permanent symptoms such as deafness and mental retardation in 40% of cases - Both primary measles (giant cell) pneumonia and secondary bacterial pneumonia may occur - Bacterial otitis media is quite common - Subacute sclerosing panencephalitis (SSPE) is a rare, fatal disease of the CNS that occurs several years after measles infection * Measles in pregnant women leads to an increased risk of stillbirth rather than congenital abnormalities * Atypical measles occurs in some people who were infected with measles after being given the killed vaccine, and it is characterized by an atypical rash without Koplik‘s spots * Most diagnosis are made on clinical grounds, but isolation of the virus and a rise in antibody titer can be used to diagnose difficult cases * There is no antiviral therapy available * Prevention rests on immunization with the live, attenuated vaccine that is typically given in combination with rubella and mumps vaccines (MMR vaccine)

Answer 62

Poliovirus is a picornavirus. Picornaviruses are small (20-30 nm) non-enveloped viruses composed of an icosahedral nucleocapsid and single-stranded, positive-polarity RNA genome. Poliovirus (Picornaviridae) * Poliovirus causes poliomyelitis * There are three serologic types of poliovirus based on different antigenic determinants on the outer capsid proteins * The virion interacts with specific cell receptors on the cell membrane to enter the cell - After uncoating, the RNA genome functions as mRNA and is translated to one very large polypeptide - That polypeptide eventually forms both the capsid proteins of the progeny virions and several non-capsid proteins, including the viral RNA polymerase that synthesizes the progeny RNA genomes - Virions accumulate in the cell cytoplasm and are released upon death of the cell * Poliovirus is transmitted by the fecal-oral route * After replicating in the oropharynx and small intestine, especially in lymphoid tissue, the virus spreads through the bloodstream (or retrograde along nerve axons) to the CNS - In the CNS, poliovirus preferentially replicates in the motor neurons located in the anterior horn of the spinal cord § Death of these cells leads to paralysis of the muscles innervated by them - The virus also affects the brainstem, leading to “bulbar“ poliomyelitis (with respiratory paralysis), but rarely damages the cerebral cortex * The range of responses to poliovirus infection includes (1) inapparent, asymptomatic infection; (2) abortive poliomyelitis; (3) non-paralytic poliomyelitis; and (4) paralytic poliomyelitis - Asymptomatic infection is quite common, with only ~1% of infections being clinically apparent - The most common clinical form is abortive poliomyelitis, which is a mild, febrile illness characterized by headache, sore throat, nausea, and vomiting § Spontaneous recovery usually occurs - Non-paralytic poliomyelitis manifests as aseptic meningitis with fever, headache, and a stiff neck § Also usually resolves spontaneously - In paralytic poliomyelitis, flaccid paralysis is the predominant finding, but brainstem involvement can lead to life-threatening respiratory paralysis as well § Motor nerve damage is permanent, but some recovery of muscle function occurs as other nerve cells take over * The incubation period of the virus is usually 10-14 days * A postpolio syndrome has been described, characterized by a marked deterioration (with unknown cause) of the residual function of the affected muscles occurring many years after the acute phase * Diagnosis is made either by isolation of the virus or by a rise in antibody titer * There is no antiviral therapy and only symptomatic relief and respiratory support can be provided, if needed * Poliomyelitis can be prevented by both the killed vaccine (Salk vaccine, inactivated vaccine, IPV) and the live, attenuated vaccine (Sabin vaccine, oral vaccine, OPV), both containing all three serotypes - The live vaccine was previously favored due to its many advantages (see topic #6), but has seen less use recently due to incidences of reverting back to virulence

Answer 63

Coxsackievirus A & B (Picornaviridae) Coxsackie viruses * Coxsackie viruses are picornaviruses that cause a variety of disease - Group A viruses cause, for example, herpangina, acute hemorrhagic conjunctivitis, and hand-foot-and-mouth disease - Group B viruses cause pleurodynia, myocarditis, and pericarditis - Both types cause non-specific upper respiratory tract disease (common cold), febrile rashes, aseptic meningitis, mild paresis, and acute flaccid paralysis * Coxsackie viruses and echoviruses together cause ~90% of cases of viral meningitis * At least 24 serotypes of Coxsackie A virus and 6 serotypes of Coxsackie B virus are recognized * Replication is similar to that of polioviruses * Coxsackie viruses are transmitted primarily by the fecal-oral route, but respiratory aerosols also play a role * Group A viruses have a predilection for skin and mucous membranes, whereas group B viruses cause disease in various organs such as the heart, pleura, pancreas, and liver * Both group A and B viruses can affect the meninges and the motor neurons (anterior horn cells) to cause paralysis * From their original site of replication in the oropharynx and gastrointestinal tract, they disseminate via the bloodstream * Herpangina is characterized by fever, sore throat, and tender vesicles in the oropharynx * Hand-foot-and-mouth disease is characterized by a vesicular rash on the hands and feet and ulcerations in the mouth, mainly in children * Pleurodynia (Bornholm disease, epidemic myalgia, “devil‘s grip“) is characterized by fever and severe pleuritic-type chest pain - Not that pleurodynia is pain due to an infection of the intercostal muscles (myositis), not of the pleura * Myocarditis and pericarditis are characterized by fever, chest pain, and signs of congestive heart failure - Dilated cardiomyopathy is a feared complication * Diagnosis is made either by isolating the virus in cell culture or suckling mice or by observing a rise in antibody titer - PCR assay can be done for rapid diagnosis of viral meningitis * There is neither an antiviral drug therapy nor a vaccine available Echoviruses * Echoviruses are picornaviruses that cause a variety of diseases such as aseptic meningitis, upper respiratory tract infection, febrile illness with and without rash, infantile diarrhea, and hemorrhagic conjunctivitis * More than 30 serotypes have been isolated * Echoviruses are transmitted by the fecal-oral route and occur worldwide * The replicative cycle and pathogenesis of echoviruses is similar to that of other enteroviruses (subgroup of picornaviruses) * Diagnosis is made by isolation of the virus in cell culture * There is no antiviral therapy or vaccine available Rhinovirus (Picornaviridae) Rhinoviruses * Rhinoviruses are the main cause of the common cold * There are more than 100 serologic types, which explains why the common cold is so common * Rhinoviruses replicate better at 33°C than at 37°C and therefore affect primarily the nose and conjunctiva, rather than the lower respiratory tract * Because they are acid-labile, they are killed by gastric acid when swallowed * Replication and structure is similar to that of other picornaviruses - The cell surface receptor for rhinoviruses is intracellular adhesion molecule 1 (ICAM-1), an adhesion protein located on the surface of many types of cells * Rhinoviruses can be transmitted directly, via respiratory droplets, or indirectly, in which respiratory droplets are deposited on fomites and then transported by fingers to the nose or eyes * The portal of entry is the upper respiratory tract, and the infection is limited to that region * After an incubation period of 2-4 days, sneezing, nasal discharge, sore throat, cough, and headache are common, lasting for ~1 week * No specific antiviral therapy or vaccine is available

Answer 64

Reoviridae (Rotavirus, Colorado tick fever virus) Rotaviruses * Rotavirus is a reovirus that is a common cause of viral gastroenteritis, especially in young children * Rotavirus has a segmented, double-stranded RNA genome surrounded by a double-layered icosahedral capsid without an envelope * There are at least six serotypes of human rotavirus - The outer surface protein (also known as viral hemagglutinin) is the type-specific antigen and elicits protective antibody * Rotavirus attaches to the cell surface at the site of the β-adrenergic receptor - After entry of the virion into the cell, the RNA-dependent RNA polymerase of the virus synthesizes mRNA from each of the 11 segments within the cytoplasm - After replication of the genome for progeny virions, capsid proteins form around the newly synthesized RNA and the virus is released from the cytoplasm by lysis of the cell * Rotavirus is transmitted by the fecal-oral route and replicates in the mucosal cells of the small intestine, resulting in the excess secretion of fluids and electrolytes into the bowel lumen - No inflammation occurs, and the diarrhea is non-bloody - It is thought that the watery diarrhea is caused primarily by the stimulation of the enteric nervous system - Nausea and vomiting usually accompany the diarrhea * Diagnosis is most often made on clinical grounds, but can be made in the laboratory by detection of rotavirus in the stool by using radioimmunoassay or ELISA * There are two rotavirus vaccines available, both containing live virus and given orally - One is a live, attenuated vaccine containing the single most common rotavirus serotype (G1) causing disease in the US - The other is a live reassortant vaccine containing five rotavirus strains Norovirus/Norwalk virus (Caliciviridae) Caliciviruses Caliciviruses are small, non-enveloped viruses with a single-stranded RNA genome of positive polarity and an icosahedral nucleocapsid. Norovirus is the main human pathogen in the calicivirus family. * Norovirus is one of the most common causes of viral gastroenteritis in adults worldwide * There are many serotypes of norovirus; the exact number is uncertain * Norovirus is transmitted by the fecal-oral route, often involving the ingestion of contaminated seafood or water * Infection is enhanced by the low infectious dose of the virus, excretion of the virus in the stool both before the onset of symptoms and for several weeks after recovery, and resistance to inactivation by chlorination and to drying in the environment * Norovirus infection is typically limited to the mucosal cells of the intestinal tract * Disease is characterized by sudden onset of vomiting and diarrhea accompanied by low- grade fever and abdominal cramping - Neither the emesis nor the stool contains blood - The illness typically lasts 2-3 days, and there are no long-term symptoms (except in some immunocompromised patients in whom chronic gastroenteritis can occur) - In some outbreaks, certain patients manifest signs of CNS involvement (headache, meningismus, photophobia, and obtundation Diagnosis is often a clinical one, but a PCR-based test on the stool can be performed when required * There is no antiviral therapy or vaccine available Astroviruses * Astroviruses cause watery diarrhea * They are non-enveloped RNA viruses with an icosahedral capsid and a characteristic five- or six-pointed morphology * They are similar in size to polioviruses (28-30 nm) * Transmission is via the fecal-oral route and the incubation period is 3-4 days * They typically only cause symptoms in very young or very old persons and the immunosuppressed - Symptoms are usually milder than in case of rotavirus infection and last for ~5 days * Diagnosis can be done with serologic tests and PCR assay * There is no antiviral therapy or vaccine available

Answer 65

Rabies virus (Rhabdoviridae) * Rabies virus causes rabies, a type of encephalitis * Rabies virus is the only medically important member of the rhabdovirus family * It has a single-stranded RNA genome with a negative-polarity enclosed within a bullet- shaped capsid surrounded by a lipoprotein envelope * Rabies virus has a single antigenic type and a broad host range * Rabies virus attaches to the acetylcholine receptor on the cell surface - After entry into the cell, the virion RNA polymerase synthesizes mRNAs that code for viral proteins - After replication of the genome viral RNA by a virus-encoded RNA polymerase, progeny RNA is assembled with virion proteins to form the nucleocapsid, and the envelope is acquired as the virion buds through the cell membrane * The virus is transmitted by the bite of a rabid animal that manifests aggressive, biting behavior induced by the viral encephalitis - These animals include skunks, raccoons, bats, cats, and dogs * Worldwide, approximately 50,000 people die of rabies each year * The virus multiplies locally at the bite site, infects the sensory neurons, and moves by axonal transport to the CNS - The virus multiplies in the CNS and then travels down the peripheral nerves to the salivary glands and other organs - From the salivary glands, it enters the saliva to be transmitted by the bite * Within the CNS, encephalitis develops with the death of neurons and demyelination - Infected neurons contain an eosinophilic cytoplasmic inclusion called a Negri body * The incubation period varies, according to the distance from the location of the bite to the CNS, from as short as 2 weeks to 16 weeks or longer - Prodromal non-specific symptoms such as fever, anorexia, and changes in sensation at the bite are typical after the incubation period - After the prodrome, rabies manifests as either of two forms a) “Furious“ (encephalitic) – 80% of cases; agitation, delirium, seizures, and hydrophobia occur b) “Dumb“ (paralytic) – 20% of cases; spinal cord is primarily involved; ascending paralysis occurs - Death almost invariably occurs following both forms * Rapid diagnosis of rabies infection in the animal is usually made by examination of brain tissue by using either PCR assay, fluorescent antibody to rabies virus, or histologic staining of Negri bodies in the cytoplasm of hippocampal neurons * Rabies in humans can be diagnosed by PCR assay, by fluorescent antibody staining of a biopsy specimen, by isolation of the virus, or by a rise in antibody titer to the virus * Rabies can be prevented before exposure with the killed virus vaccine, and postexposure with the use of both the vaccine and human rabies immune globulin (RIG) plus an immediate cleaning of the wound

Answer 66

Togaviridae (Rubella virus, Arbovirus) * Rubella virus causes rubella and congenital rubella syndrome, the latter of which is characterized by congenital malformations * Rubella virus is a togavirus composed of a single-stranded RNA with a positive-polarity, an icosahedral nucleocapsid, and a lipoprotein envelope - Its surface spikes contain hemagglutinin * After penetration of the cell and uncoating, the plus-strand RNA genome is translated into several non-structural and structural proteins - One of the non-structural proteins is an RNA-dependent RNA polymerase, which replicates the genome for the virion progeny - Both replication and assembly occur in the cytoplasm, and the envelope is acquired from the outer membrane as the virion exits the cell * The virus is transmitted via respiratory droplets and from mother to fetus transplacentally * The disease occurs worldwide and epidemics occur every 6-9 years in areas where the vaccine is not used * Initial replication of the virus occurs in the nasopharynx and local lymph nodes - From there, it spreads via the blood to the internal organs and skin * Natural infection leads to lifelong immunity * Rubella is a milder, shorter disease than measles - After an incubation period of 14-21 days, a brief prodromal period with fever and malaise is followed by a maculopapular rash, which starts on the face and progresses downward to involve the extremities - Posterior auricular lymphadenopathy is characteristic - The rash typically lasts 3 days - Polyarthritis caused by immune complexes often occurs in adults, especially women * When a non-immune pregnant woman is infected during the first trimester, especially the first month, significant congenital malformations can occur as a result of maternal viremia and fetal infection - The malformations primarily involve the heart (e.g. patent ductus arteriosus), the eyes (e.g. cataracts), and the brain (e.g. deafness and mental retardation) * Rubella virus can be grown in cell cultures, and is identified by its ability to interfere with the cytopathic effect of echoviruses - Diagnosis can also be made by observing a 4x or greater rise in antibody titer or by PCR assay * There is no antiviral therapy * Prevention involves immunization with the live, attenuated vaccine that is usually given in combination with the measles and mumps vaccines (MMR vaccine) * Immune serum globulins (IG) can be given to pregnant women who have been exposed to a known case of rubella and for whom termination of the pregnancy is not an option

Answer 67

Hepatitis A virus (Picornaviridae) Hepatitis A virus (HAV) * HAV causes hepatitis A * HAV is a typical enterovirus classified in the picornavirus family (single-stranded RNA genome, non-enveloped, icosahedral nucleocapsid, replication in cytoplasm) * Its replicative cycle is similar to that of polioviruses * HAV is transmitted by the fecal-oral route and humans are the only reservoir * Children are the most frequently infected group, and outbreaks occur in special living situations such as summer camps and boarding schools * The pathogenesis of HAV infection is not completely understood, but it is thought to replicate in the GI tract and then spread to the liver via the blood - Hepatocytes are infected, and it is likely that attack by cytotoxic T cells causes the damage to hepatocytes - Infection is cleared, the damage is repaired, and no chronic infection ensues * The clinical manifestations of hepatitis are virtually the same, regardless of which hepatitis virus is the cause - Symptoms include fever, anorexia, nausea, vomiting, and jaundice - Dark urine, pale feces, and elevated transaminase levels are seen * Hepatitis A has a an incubation period of 3-4 weeks and most infections are asymptomatic * The detection of IgM antibody is the most important test for diagnosis * No antiviral therapy is available, but a vaccine containing inactivated HAV is * Immune globulins given prior to infection or within 14 days after exposure can prevent or mitigate the disease Hepatitis E virus (HEV) * HEV is a major cause of hepatitis transmitted by the fecal-oral route * It is a non-enveloped, single-stranded RNA virus classified as a member of the hepevirus family * Clinically, the disease resembles hepatitis A, with the exception of a high mortality rate in pregnant women * Chronic infection, resulting in chronic hepatitis and cirrhosis but no hepatocellular carcinoma, occurs in immunocompromised individuals * Diagnosis is typically made by detecting IgM antibody to HEV, but a PCR assay is also available * There is no antiviral drug available, but ribavirin can be used in immunocompromised patients to clear HEV viremia * There is no vaccine

Answer 68

Hepatitis B virus (Hepadnaviridae) Hepatitis B virus (HBV) * HBV causes hepatitis B * HBV is a member of the hepadnavirus family * It has a 42-nm enveloped virion, with an icosahedral nucleocapsid core containing a partially double-stranded circular DNA genome - The envelope contains a particle called the surface antigen (HBsAg) - In addition to HBsAg, there are two other important antigens located in the core of the virus: the core antigen (HBcAg) and the e antigen (HBeAg) * After entry of the virion into the cell and its uncoating, the nucleocapsid moves to the nucleus, where the virion DNA polymerase synthesizes the missing portion of DNA to form a double-stranded circular DNA - The double-stranded DNA serves as a template for mRNA synthesis by cellular RNA polymerase as well as full-length RNA that will serve as a template for the virion progeny genome - RNA-dependent DNA synthesis catalyzed by reverse transcriptase encoded by HBV takes place within the newly assembled virion nucleocapsid core in the cytoplasm - Progeny HBV with its HBsAg-containing envelope are released from the cell by budding through the cell membrane * The three main modes of transmission are via blood, during sexual intercourse, and perinatally from mother to newborn - HBV infection is especially prevalent in addicts who use IV drugs * Hepatitis B is found worldwide but is particularly prevalent in Asia After entering the blood, the virus infects hepatocytes, and viral antigens are displayed on the surface of the cells - Cytotoxic T cells mediate an immune attack against the viral antigens, and inflammation and necrosis occur * About 5% of adult patients with HBV infection become chronic carriers, whereas the ratio in infected newborns is around 90% - Chronic infection is marked by the persistence of HBsAg in the blood for 6 months or longer - A high rate of hepatocellular carcinoma (HCC) occurs in chronic carriers * Many HBV infections are asymptomatic * The mean incubation period for hepatitis B is 10-12 weeks * The clinical appearance of hepatitis B is similar to that of hepatitis A, but symptoms tend to be more severe and life-threatening hepatitis can occur * The two most important serologic tests for the diagnosis of early hepatitis B are the tests for HBsAg and for IgM antibody to the core antigen (HBcAb) - There is a period of several weeks when HBsAg has disappeared but HBsAb is not yet detectable called the window phase, and at this time the HBcAb can be used to make the diagnosis - The presence of HBeAg in chronic carriers indicates a high likelihood of transmissibility * No antiviral therapy is typically used in acute hepatitis B, but for chronic hepatitis B entecavir or tenofovir are the drugs of choice * Prevention involves the use of either the vaccine or hyperimmune globulin or both - The vaccine contains HBsAg and is highly effective - Hepatitis B immune globulin (HBIG) contains a high titer of HBsAb and is used to provide immediate, passive protection to individuals known to be exposed to HBsAg-positive blood Hepatitis D virus (HDV) * HDV causes hepatitis D * HDV is unusual in that it is a defective virus, i.e. it cannot replicate by itself because it does not have the genes for its envelope protein - HDV can replicate only in cells also infected with HBV because HDV uses the HBsAg as its envelope protein * HDV is an enveloped virus with a single-stranded, negative-polarity RNA genome, which is very small and encodes only one protein (the internal core protein called delta antigen) * The virus is transmitted by the same means as is HBV * It seems likely that the pathogenesis of hepatitis caused by HDV and HBV is the same * A person can either be infected with both HDV and HBV at the same time (i.e. be “coinfected“) or be previously infected with HBV and then “superinfected“ with HDV - Hepatitis in patients coinfected with HDV and HBV is more severe than in those infected with HBV alone, but the incidence of chronic hepatitis is the same - Hepatitis in chronic carriers of HBV who become superinfected with HDV is much more severe, and the incidence of fulminant, life-threatening hepatitis, chronic hepatitis, and liver failure is significantly higher * The diagnosis of HDV infection in the laboratory is made by detecting either delta antigen or IgM antibody to delta antigen in the patient‘s serum * Interferon-α can mitigate some of the effects of chronic hepatitis D, but there is no specific antiviral therapy or vaccine against HDV Hepatitis C virus (Flaviviridae) Hepatitis C virus (HCV) * HCV causes hepatitis C * HCV is a member of the flavivirus family * It is an enveloped virus containing a single-stranded, positive-polarity RNA genome * HCV has at least six genotypes and multiple subgenotypes * The replication of HCV is uncertain because it has not been grown in cell culture, but other flaviviruses replicate in the cytoplasm - A virion encoded protease cleaves the functional viral proteins and is the target of potent anti-HCV therapy - The genome also encodes another target of anti-HCV therapy, a protein called NS5A that co-operates with the RNA polymerase of the virus to synthesize progeny genome RNA‘s * HCV is transmitted primarily via blood, but also from mother to child during birth and via sexual transmission * It infects hepatocytes primarily, and death of the hepatocytes is probably caused by immune attack by cytotoxic T cells * HCV infection strongly predisposes to hepatocellular carcinoma * Antibodies against HCV are made, but ~75% of patients are chronically infected and continue to produce the virus for at least 1 year - Chronic active hepatitis and cirrhosis occur in ~10% of these patients - Chronic infection is characterized by elevated transaminase levels, a positive ELISA antibody test, and detectable viral RNA for at least 6 months * The acute infection is often asymptomatic, and if symptoms such as malaise, nausea, and right upper quadrant pain do occur, they are milder than in other types of viral hepatitis - Otherwise, the clinical picture resembles hepatitis B - HCV infection also leads to significant autoimmune reactions, including vasculitis, arthralgias purpura, and membranoproliferative glomerulonephritis * HCV infection is diagnosed by detecting antibodies to HCV in an ELISA test - The test does not distinguish between an acute, chronic, or resolved infection - PCR assay detecting the presence of viral RNA (viral load) in the serum should be performed in case of positive ELISA to determine whether active disease exists * Treatment of acute hepatitis C with interferon-α significantly decreases the number of patients who become chronic carriers * The treatment of choice for chronic hepatitis C is a combination of drugs from three classes (1) RNA polymerase inhibitors (e.g. sofosbuvir) (2) NS5A inhibitors (e.g. velpatasvir) (3) Protease inhibitors (e.g. grazoprevir) * There is no vaccine and hyperimmune globulins are not available

Answer 69

Arbovirus is an acronym for arthropod-borne virus and highlights the fact that these RNA viruses are transmitted by arthropods, primarily mosquitoes and ticks. Most arboviruses are classified into three families, namely togaviruses, flaviviruses, and bunyaviruses. Togaviruses are characterized by an icosahedral nucleocapsid surrounded by an envelope and a single-stranded, positive-polarity RNA genome. Flaviviruses are similar to togaviruses but smaller in diameter (40-50 nm compared to 70 nm). Bunyaviruses have a helical nucleocapsid surrounded by an envelope and a genome consisting of three segments of negative-polarity RNA. Most human arboviral infections are asymptomatic. Of those infections that are symptomatic, the clinical picture usually fits one of three categories: (1) encephalitis; (2) hemorrhagic fever; or (3) fever with myalgias, arthralgias, and non-hemorrhagic rash. Humans are usually dead-end hosts, but can act as reservoirs in some diseases (e.g. yellow fever and dengue) where there is a high level of viremia. The arboviruses that cause encephalitis include the Eastern equine encephalitis virus (EEEV), Western equine encephalitis virus (WEEV), St. Louis encephalitis virus (SLEV), California encephalitis virus (CEV), West Nile virus (WNV), Japanese encephalitis virus (JEV), and tick-borne encephalitis viruses. They are all diagnosed by either isolating the virus or demonstrating a rise in antibody titer, and no antiviral therapy or human vaccine exists for most of them at present. Eastern equine encephalitis virus (EEEV) * EEEV is a togavirus that causes the most severe disease and is associated with the highest fatality (~50%) among arboviruses causing encephalitis * Transmitted primarily by the swamp mosquito and has a wild bird reservoir * The encephalitis is characterized by the sudden onset of severe headache, nausea, vomiting, and fever - Changes in mental status (confusion, stupor) ensue - A rapidly progressive downhill course with nuchal rigidity, seizures, and coma occurs - If the patient survives, the CNS symptoms are usually severe Western equine encephalitis virus (WEEV) * WEEV is a togavirus that causes disease more frequently than EEE virus, but the illness is less severe (fatality rate of ~2%) * The virus is transmitted primarily by mosquitoes among the wild bird population of endemic areas * The clinical picture is similar but less severe than that caused by EEE virus St. Louis encephalitis virus (SLEV) * SLEV is a flavivirus that causes disease over a wider geographic area than EEEV and WEEV * Transmission is primarily by mosquitoes and the reservoir is wild birds * Causes moderately severe encephalitis with a fatality rate of ~10% * Most infections are asymptomatic California encephalitis virus (CEV) * CEV is a bunyavirus that is transmitted by mosquitoes among forest rodents * The clinical picture can be mild, resembling entoviral meningitis, or severe, resembling herpes encephalitis, but death rarely occurs West Nile virus (WNV) * WNV is the most common cause of neuroinvasive (encephalitis, meningitis) arboviral disease in the US * WNV is a flavivirus that is endemic in Africa but has caused encephalitis in areas of Europe and Asia as well * Wild birds are the main reservoir of this virus, which is transmitted by mosquitoes * The most important clinical picture is encephalitis with or without signs of meningitis, typically in a person over 60 years of age - Encephalitis occurs in ~1% of infections, fever and headache without encephalitis in ~20%, and ~80% of infections are asymptomatic Japanese encephalitis virus (JEV) * JEV is the most common cause of epidemic encephalitis in rural areas of Asia * It is a member of the flavivirus family and is transmitted to humans by mosquitoes endemic to Asian rice fields * There are two main reservoir hosts–birds and pigs * The mortality rate is high (~40%), and neurologic symptoms are severe and can be detected in most survivors * An inactivated vaccine is available and recommended for individuals living in areas of endemic infection for several months or longer Tick-borne encephalitis viruses * These viruses belong to the family of flaviruses and cause Central European tick-borne encephalitis, Russian spring-summer encephalitis, Powassan encephalitis, and louping-ill * Reservoirs are rodents, goats, sheep, and ticks (also act as vectors) * The disease follows a biphasic pattern and the median incubation period is 8 days after the tick bite - Non-specific symptoms such as mild fever, malaise, headache, nausea, vomiting, and myalgias may be present and resolve within a week - After another week the patient may develop neurological symptoms (encephalitis, meningitis, meningoencephalitis) * Louping-ill is an acute viral disease primarily of sheep in the UK

Answer 70

Flaviviridae overview Yellow fever virus * Yellow fever virus causes yellow fever, a disease characterized by jaundice and fever - It is a severe, life-threatening disease that begins with the sudden onset of fever, headache, myalgias, and photophobia, and then progresses to involve the liver, kidneys, and heart - Prostration, shock, and upper GI tract hemorrhage with hematemesis occur * Yellow fever occurs primarily in the tropical areas of Africa and South America * Two distinct epidemiological cycles exist in nature, with different reservoirs and vectors (1) Jungle yellow fever is a disease of monkeys in tropical Africa and South America; it is transmitted primarily by mosquitoes and humans are accidental hosts (2) Urban yellow fever is a disease of humans that is transmitted by a different species of mosquitoes * Diagnosis in the laboratory can be made either by isolating the virus or by detecting a rise in antibody titer * No antiviral therapy is available and the mortality rate is high, but lifelong immunity is conferred if the patient survives * Travelers to and residents of endemic areas should be immunized with the vaccine containing live, attenuated yellow fever virus Dengue virus * Dengue virus causes dengue fever, the most common insect-borne viral disease in the world * Classic dengue fever (breakbone fever) begins suddenly with an influenza-like syndrome consisting of fever, malaise, retro-orbital pain, and headache - Severe myalgia and arthralgia occur - Enlarged lymph nodes, facial flushing, a maculopapular rash, and leukopenia are common - After a week or so, the symptoms regress but weakness may persist * Dengue hemorrhagic fever is a much more severe disease, with a fatality rate that approaches 10% - The initial picture is the same as classic dengue, but then shock and hemorrhage, especially into the GI tract and skin, develop - Hemorrhagic shock syndrome is due to the production of large amounts of cross-reacting antibody at the time of a second dengue infection * Dengue virus is transmitted by mosquitoes and humans are the reservoir * Diagnosis is made in the same way as with yellow fever * There is no antiviral therapy or vaccine available for dengue

Answer 71

Robovirus is an acronym for rodent-borne virus and refers to the fact that these viruses are transmitted directly from rodents to humans without an arthropod vector. Hantaviruses * Hantaviruses are members of the bunyavirus family * The prototype virus is Hantaan virus, the cause of Korean hemorrhagic fever (KHF) - KHF is characterized by headache, petechial hemorrhages, shock, and renal failure - The disease occurs in Asia and Europe and has a mortality rate of 10% * Sin Nombre virus is another hantavirus that causes hantavirus pulmonary syndrome, a disease characterized by influenza-like symptoms followed rapidly by acute respiratory failure - The virus is endemic in deer mice and is acquired by inhalation of aerosols of the rodent‘s urine and feces - There is no effective antiviral drug and the mortality rate is ~35% - Diagnosis is made with PCR assay or serological tests * There is no vaccine for any hantavirus Lymphocytic choriomeningitis virus (Arenaviridae) LCM virus * Lymphocytic choriomeningitis (LCM) virus is a member of the arenavirus family, which are enveloped viruses with surface spikes, a helical nucleocapsid, and a single-stranded RNA genome with negative-polarity It is a rare cause of aseptic meningitis and cannot be clinically distinguished from the more frequent viral causes (e.g. echovirus, Coxsackie virus, or mumps virus) * The virus is endemic in the mouse population and it is transmitted to humans via food or water contaminated by mouse urine or feces * Diagnosis is made by isolating the virus from the spinal fluid or by detecting an increase in antibody titer * No antiviral therapy or vaccine is available Lassa fever virus * Lassa fever virus causes a severe hemorrhagic fever characterized by multiorgan involvement - The disease begins slowly with fever, headache, vomiting, and diarrhea and progresses to involve the lungs, heart, kidneys, and brain - A petechial rash and GI tract hemorrhage ensue, followed by death from vascular collapse in ~20% of cases * Lassa fever virus is a member of the arenavirus family, like LCM virus * The natural hosts for Lassa fever virus are a certain genus of mice and the virus is transmitted to humans by contamination of food or water with animal urine * Asymptomatic infection is widespread in areas of endemic infection * Diagnosis is made either by isolating the virus or by detecting a rise in antibody titer * Ribavirin reduces the mortality rate if given early, and hyperimmune serum (obtained from persons who have recovered from the disease) has been beneficial in some cases * No vaccine is available Filoviridae (Ebolavirus, Marburgvirus) There are two important filoviruses that cause human disease: Ebola virus and Marburg virus. Ebola virus * Ebola virus causes Ebola hemorrhagic fever (EHF) * It has a single-stranded, non-segmented, negative-polarity RNA genome and a helical nucleocapsid * After the virion enters the cytoplasm, the virion RNA polymerase transcribes the genome into mRNAs - The RNAs are translated, the progeny genome is synthesized by the virus-encoded RNA polymerase, and after assembly of the progeny virion it buds from the surface of the infected cell * The natural reservoir of Ebola virus is unknown, but fruit bats and rodents are the prime suspects * Transmission from human to human occurs via blood and body fluids * The high mortality rate of Ebola virus (up to 90%) is attributed to several virulence factors - Its glycoprotein kills endothelial cells, resulting in hemorrhage, and two other proteins inhibit the induction and action of interferon * The incubation period is typically 5-7 days but may be up to 21 days * EHF begins with a constellation of symptoms such as fever, headache, sore throat, myalgia, arthralgia, epigastric pain, vomiting, and diarrhea - Later, bleeding into the skin and GI tract occurs, followed by shock and DIC leading to multiorgan failure - The hemorrhages are a result of both severe thrombocytopenia and death of endothelial cells - Marked lymphopenia also occurs * Diagnosis is often made by detecting viral antigens in serum using ELISA, by detecting viral RNA using a PCR assay, or by detecting IgM antibody in the serum - Extreme care must be taken when handling specimens in the laboratory * No antiviral therapy or vaccine is available Marburg virus * Marburg virus and Ebola virus are similar in that they both cause hemorrhagic fever and are members of the filovirus family; however, they are antigenically distinct

Answer 72

Slow virus infections 1) Progressive multifocal leukoencephalopathy (PML) * Fatal demyelinating disease of the white matter (i.e. leukoencephalopathy) caused by JC virus, a member of the polyomavirus family - Polyomaviruses are non-enveloped viruses with a circular, double-stranded DNA genome * JC virus infects and kills oligodendroglia, causing demyelination * The clinical picture includes visual field defects, mental status changes and weakness - The disease rapidly progresses to blindness, dementia, and coma, and most patients die within 6 months * The disease occurs primarily in patients with compromised cell-mediated immunity * Diagnosis is typically made by PCR assay of a brain biopsy specimen or spinal fluid * There is no effective antiviral treatment, but cidofovir may be beneficial 2) Subacute sclerosing panencephalitis (SSPE) * Slowly progressive disease characterized by inflammatory lesions in many areas of the brain * It is a rare disease of children who were infected by measles virus several years earlier * SSPE begins with mild changes in personality and ends with dementia and death 3) Acquired immunodeficiency syndrome (AIDS) * AIDS is a disease caused by HIV with a long latent period and a progressive course that can involve the CNS (See topic #29 for more information) Prions and prion-caused diseases Prions are protein-containing particles that are highly resistant to inactivation by heat, formaldehyde, and UV light. The normal prion protein (PrPC) only causes disease when the normal alpha-helical conformation changes to a beta-pleated sheet (PrPSC). These abnormal forms aggregate into filaments, which disrupt neuron function and cause cell death. The human prion-mediated diseases (e.g. kuru and CJD) are called transmissible spongiform encephalopathy (TSE), in reference to the spongiform changes that occur as a result of neuronal vacuolation and loss. Prion-caused diseases can be classified into three categories: (1) transmissible (infectious), such as kuru; hereditary (genetic), such as fatal familial insomnia; and sporadic, such as most forms of CJD. 1) Kuru * Fatal disease characterized by progressive tremors and ataxia but not dementia * Occurs only among the Fore tribes in New Guinea, and was transmitted during a cannibalistic ritual 2) Creutzfeldt-Jakob disease (CJD) * Found sporadically worldwide, most cases occur in people who are 50-70 years old * Has been transmitted iatrogenically, e.g. in a corneal transplant and via intracerebral electrodes * There is only one confirmed case of CJD being transmitted by blood transfusion * The main clinical findings are dementia (including behavioral changes, memory loss, and confusion) and myoclonic jerking - Additional findings include ataxia, aphasia, visual loss, and hemiparesis * Symptoms typically appear gradually and progress inexorably * In the terminal stage, the patient becomes mute and akinetic, and then comatose * About 80% of those affected die within 1 year * A presumptive diagnosis of CJD can be made by detecting spongiform changes in a brain biopsy specimen, and specific diagnosis is typically made by using anti-prion antibodies to stain the patient‘s brain specimen * Although most cases are sporadic, about 10% are hereditary * There is no treatment or vaccine available 3) Variant Creutzfeldt-Jakob disease (vCJD) * Hypothesized to originate from consumption of beef contaminated with mutated prions responsible for mad cow disease * It is unknown how many people harbor the pathogenic prion in a latent (asymptomatic) form

Answer 73

Human papillomavirus (HPV) * HPV causes papillomas, which are benign tumors of squamous cells - Some HPV types, especially types 16 and 18, cause carcinoma of the cervix, penis, and anus * Papillomaviruses are non-enveloped viruses with double-stranded circular DNA and an icosahedral nucleocapsid * Two of the early genes synthesized by HPV, namely E6 and E7, are implicated in carcinogenesis through inactivation of the p53 gene and retinoblastoma (RB) gene * There are at least 100 types of papillomaviruses, and there is a pronounced predilection of certain types to infect certain tissues * After attachment and uncoating, the DNA genome moves to the nucleus - mRNA is synthesized by host cell RNA polymerase and then the progeny DNA genomes are synthesized by the host cell DNA polymerase * Papillomaviruses are transmitted primarily by skin-to-skin contact, * They infect squamous epithelial cells and induce within those cells a characteristic perinuclear cytoplasmic vacuole - These vacuolated cells are called koilocytes * Papillomas of various organs are the predominant finding - Skin and plantar warts are caused primarily by HPV-1 through HPV-4 - Genital warts (condylomata acuminata) are caused primarily by HPV-6 and HPV-11 § HPV-6 and HPV-11 also cause respiratory tract papillomas, especially laryngeal papillomas, in young children * Carcinoma of the uterine cervix, the penis, and the anus (as well as premalignant lesions called intraepithelial neoplasia) are associated with infection by HPV-16 and HPV-18 - HPV-16 is also implicated as the cause of oral cancers * Infections are usually diagnosed clinically, but a PCR assay can be used to detect 14 high-risk genotypes, including HPV-16 and HPV-18 * The usually treatment for genital warts is podophyllin, but interferon-α is also effective and is better at preventing recurrences * Liquid nitrogen is commonly used for skin warts * Cidofovir may be useful in the treatment of severe HPV infections * There are three vaccines against HPV: (1) one against types 6, 11, 16, and 18, as well as five other serotypes; (2) one against types 6, 11, 16, and 18, but not the other serotypes; (3) and one that only contains the proteins of types 16 and 18 - The immunogen in the vaccine is the L1 capsid protein of each type Human T-cell lymphotropic virus (HTLV) * HTLV-1 causes a cancer called adult T-cell leukemia/lymphoma and a neurologic disease called HTLV-associated myelopathy (a.k.a. tropical spastic paresis or chronic progressive myelopathy) - HTLV-2 also appears to cause these diseases, but the association is less clearly documented * HTLV, a member of the retrovirus family, is an enveloped virus with reverse transcriptase in the virion and two copies of single-stranded, positive-polarity RNA genome * The HTLV genome contains three structural genes common to all retroviruses (gag, pol, and env) plus two regulatory genes (tax and rex) - HTLV does not have an oncogene in its genome, but rather it is the transcription upregulation by the Tax protein that initiates oncogenesis * HTLV primarily infects CD4+ T lymphocytes - Within the cytoplasm, reverse transcriptase synthesizes a DNA copy of the genome, which migrates to the nucleus and integrates into cell DNA - Viral mRNA is made by host cell RNA polymerase, and transcription is upregulated by Tax protein (as mentioned earlier) - Full-length RNA is synthesized and transported to the cytoplasm, where it is assembled into a nucleocapsid that buds out of the cell at the outer cell membrane * HTLV is transmitted primarily by IV drug use, sexual contact, or breast feeding * Infection is endemic in certain geographic areas, such as the Caribbean region, eastern South America, western Africa, and southern Japan * Adult T-cell leukemia/lymphoma (ATL) is characterized by lymphadenopathy, hepato- splenomegaly, lytic bone lesions, and skin lesions - These features are caused by proliferating T cells infiltrating these organs * The clinical features of HTLV-associated myelopathy (HAM) include gait disturbance, weakness of the lower limbs, and low back pain - Loss of motor function is much greater than sensory loss * Infection with HTLV is determined by detecting antibodies against the virus in the patient’s serum using the ELISA test, and then a Western blot assay is used to confirm a positive ELISA result * There is no specific antiviral treatment or vaccine against HTLV

Answer 74

HIV (Retroviridae) * Human immunodeficiency virus (HIV) is the cause of acquired immunodeficiency syndrome (AIDS) * HIV preferentially infects and kills CD4+ helper T lymphocytes, resulting in the loss of cell-mediated immunity and a high probability that the host will develop opportunistic infections - Other cells that express CD4 on their surfaces (e.g. macrophages) can be infected also * HIV, a retrovirus, has a cylinder-shaped core with two identical molecules of single-stranded, positive-polarity RNA that is surrounded by an envelope containing virus-specific glycoproteins (gp120 and gp41) - In addition to the three typical retroviral genes that encode structural proteins (gag, pol, and env), the RNA genome has six regulatory genes - Three enzymes are located within the nucleocapsid of the virion: reverse transcriptase (RNA-dependent DNA polymerase), integrase, and protease * The initial step in the entry of HIV into the cell is the binding of the virion gp120 envelope protein to the CD4 protein on the cell surface and interaction with one of the chemokine receptors (CXCR4 or CCR5, depending on the strain) - After fusion of the viral envelope with the cell membrane, the virion core enters the cytoplasm where reverse transcriptase transcribes the genome RNA into double-stranded DNA, which migrates to the nucleus to integrate into the host cell DNA - Viral mRNA is transcribed from the integrated DNA by host cell RNA polymerase and is then translated and cleaved to specific viral proteins * T cell-tropic strains of HIV bind to CXCR4, whereas the macrophage-tropic strains bind to CCR5 * Transmission of HIV occurs primarily by sexual contact and by transfer of infected blood - Perinatal transmission from mother to neonate, either across the placenta, at birth, or via breast milk, also occurs * The clinical picture of HIV infection can be divided into three stages: an early, acute stage; a middle, latent stage; and a late, immunodeficiency stage 1) Acute stage - Usually begins 2-4 weeks after infection - Mononucleosis-like picture of fever, lethargy, sore throat, and generalized lymphadenopathy occurs - Maculopapular rash on the trunk, arms, and legs (but sparing the palms and soles) is also seen - Leukopenia occurs, but the number of CD4+ cells is usually normal - High-level viremia typically occurs and the infection is readily transmissible during this acute stage - Usually resolves spontaneously in ~2 weeks 2) Latent stage - Long latent period, measured in years, where the patient is asymptomatic and viremia is low or absent - A large amount of HIV is being produced by lymph node cells but remains sequestered within the lymph nodes 3) Immunodeficiency stage (AIDS) - Manifests as a decline in the number of CD4+ cells to below 200/μL and an increase in the frequency and severity of opportunistic infections * The two most characteristic manifestations of AIDS are Pneumocystis pneumonia and Kaposi’s sarcoma - Other opportunistic infections, such as disseminated herpes simplex (virus), cryptococcal meningitis (fungus), toxoplasmosis (protozoan), and tuberculosis (bacterium), may also occur * The presumptive diagnosis of HIV infection is often made by the detection of antibodies in the patient’s serum to the p24 core protein of HIV using the ELISA test - The definitive diagnosis is made by Western blot analysis - During the first months after infection, antibody tests may be falsely negative due to insufficient antibody being made (PCR assay may be done in this case) * The treatment of HIV infection is complex and depends on several factors, but it usually involves a combination of two nucleoside reverse transcriptase inhibitors (2NRTIs) with either a non-nucleoside reverse transcriptase inhibitor (NNRTI), a protease inhibitor (PI), or an integrase inhibitor (II) –> 2 NRTIs + NNRTI / PI / II - Emtricitabine and tenofovir are usually the NRTIs of choice - Efavirenz is a commonly used NNRTI - Ritonavir is an example of a PI - Raltegravir can be used as an II - These combinations are known as highly active antiretroviral therapy (HAART), and they are very effective in prolonging and improving quality of life but they do not cure HIV infection

Answer 75

Container with spoon - Fill halfway Viruses = quick immunochromatography + multiplex real time pcr Bacteria = culture on special media => identification MALDI TOF parasites = protozoa= immunochromatography, PCR, Microscopy, 3x Worm eggs, larvae, segments of flatworms = microscopy

Answer 76

I.Bacteria infection = hemoculture bottles, color inside is not important, inside culturing fluid, body temp before + after - best before antibiotics treatment, if not there are granules inside sticking to it + Bacteremia suspected = sepsis patient, endocarditis patient,pneumonia, osteomyelitis + when arrived place them inside an incubator 7-10 Days to detect growth, the cloudiness, if growth detected => gotta culture, some cases do MALDI imme Case 1 MALDI TOF right away Case 2 Subculture then use MALDI TOF Case 3 check with microscope and gram stain => culturing => MALDI TOF + Some bacteria cant be/ diff to cultured => Specific antibody detection Eg = syphillis (treponema pallidum); lyme disease (borrelia) - Tube for serology = native blood => wants serum (small thin, gel at the bottom), clot activator + Bacteria + viruses = whole blood or plasma from uncog blood => used for :multiplex real time PCR => Tubes for this have= EDTA, heparin, sodium citrate II. Virus infection : usually start with serology then pcr + Serology from native blood : HIV, Hepatitis viruses, measles, mumps, rubella, varicella, EBV, CMV + PCR = EDTA blood, check the presence or viral load : HIV, Hepatitis viruses, etc; check directly for the genome + Do not culture viruses anymore in the blood III. Parasites + if it's a tissue infection or larva migration : check eosinophilia (uncog blood) + check for specific antibodies : echinococcus, extraintestinal amebiasis, toxocara, toxoplasma

Answer 77

+ Meningitis, encephalitis Bacterial infection : clear sterile fluid normally, if there are bacterias could turn cloudy = purulent meningitis + if it remains clear = aseptic meningitis + step 1 do gram stain, methylene blue stain or both because gram negative is light pink in gram stain, but will stain blue with methylene blue + light microscope + step 2 usually culturing = media, see colonies => do MALDI TOF Colonies good cuz also check antibiotic susceptibility + agglutination test as a quick test : plastic beads = antibodies which can recognize the capsule, but less common now, replaced by PCR now cuz pcr is faster + If someone has purulent meningitis has protein go up, PMN go up, glucose go down + Aseptic meningitis, clear CSF = lymphocytes go up eg TB, syphillis Viruses + causing encephalitis = herpes simplex = newborn babies or immuno def + PCR : HSV1, HSV2,VZV + causing tick encephalitis (by herpes virus) (!) Not in all cases the virus level is enough in csf => pcr negative, so if suspected use acyclovir Parasites : toxoplasma (can cause encephalitis in immuno def ppl)

Answer 78

Tissue sample : anaerobic suspected (solid), two boxes Anaerobic bacteria sent in fluid = use syringe + keep needle on syringe and send it to the lab

Answer 79

- dry swab - With transport medium but can survive cuz it wont dry out, wont x2, just surviving - Black one : active carbon particles inside : bacteria can die quickly (neisseria, diphteria,etc), improve the survival - cytobrush : mucosa surfaces = collect exfoliated epithelial cells = chlamydia, trachomatis, other std bacteria, virus (HPV), vaginal or oral samples + Swabs => culture => MALDI TOF + can use PCR if respiratory viruses, nasal viruses