Clinical microbiology involves

the study of a diverse group of microorganisms and their activities.

Eukaryotes

have a nucleus, mitochondria, rough and smooth endoplasmic reticulum, Golgi, lysosomes, division by mitosis and meiosis, and other characteristics lacking in prokaryotic organism.

Protozoa

single celled "animal-like,"

non-photosynthetic eukaryotes,

are usually motile (amoebas, ciliates, flagellates) except apicomplexa.

May have trophozoite and resistant cyst forms. Important human pathogens:

Giardia Lamblia

acute or chronic foul-smelling diarrhea, usually water-borne 

(Protozoa)

Entamoeba histoyltica

amoebic dysentery (blood and pus due to colonic damage);

extraintestinal (liver abscess most common)

(Protozoa)

Naegleria fowleri

free-living amoeba;

fatal amoebic meningoencephalitis;

enter through nose whenswimming in contaminated fresh water 

(Protozoa)

Trichomonas vaginalis

common cause of sexually transmissible vaginitis

(Protoza)

Cryptosporidium

diarrhea that is self limited in normal patients;

severe and prolonged in AIDS, very young or old patients;

huge (approx. 500,000) outbreak in Milwaukee, Wisconsin in 1993

 (Protozoa)

Toxoplasma gondii

congenital infection may result in stillbirths, blindness, CNS anomalies, and other defects;

often transmitted from cats; pregnant women should avoid litter boxes

(Protozoa)

Plasmodium species

malaria; female Anopheles mosquitoes transmit

(Protozoa)

Fungi

chemoheterotrophic eukaryotic organisms with absorptive nutrition; 

most are saprophytes living off dead matter-decomposers.

Single celled microscopic budding yeasts -7 hairy molds

(filamentous septate or non-septate hypha) -7 mushrooms & puffballs.

Walls of chitin, mannans & glucans.

Divided into major groups by nature of sexual spores.

Antifungals often target ergosterol.

Candida albicans

yeast;

common cause of vaginitis (from normal flora);

oral thrush in infants; systematic infections in cancer patients; oral thrush and esophagitis in AIDS

(Fungi)

Cryptococcus neformans

encapsulated yeast;

meningitis and death,

inhalation of the organism from soil enriched with bird (pigeons) droppings;

increased incidence in cancers and AIDS

(Fungi)

Dermatophytes

(Trichopyton, Microsporum, Epidermophyton)

produce infection of superficial keratinized tissues (skin, hair, and nails),

tinea pedis, tinea corporis, tinea cruis, etc. (from others).

Fungi

Coccidiodes immitis

"valley fever",

"desert rheumatism"

flu-like illness in S.W. U.S. due to inhaled arthrospores from arid soils;

in <1% may progress to disseminated and often fatal disease; enhanced disease in pregnancy and AIDS

(Fungi)

Histoplasma capsulatum

histoplasmosis,

inhaled conidial spores from soils leads to self-limited flu-like syndrome;

<1% develop severe disseminated infection (esp. RES);

ulceration and disfigurement can occur;

enhanced in infants, elderly, and AIDS

Fungi

Pneumocystis carinii

pneumonia and occasionally systemic infections;

important cause of death in AIDS;

also occurs in other types of immunosuppression (transplants, antineoplastic therapy, corticosteroids) and malnourished infants

Fungi

Amanita phalloides

wild mushroom poisoning

(Fungi)

Helminths

multicellular eukaryotic "worms"

Example: Cestodes (tapeworms), Trematodes (flukes), Nematodes (roundworms)

Taenia saginata

beef tapeworm; ingestion of raw or undercooked beef

Cestodes (tapeworms)

Taenia solium

pork tapeworm; ingestion of raw or undercooked pork; Note: ingestion of eggs from human feces can cause systemic spread (cystercercosis)

Cestodes (tapeworms)

Schistosoma mansoni 

schistosomiasis;

snail and human host; cercariae penetrate skin;

"mask" with host antigens;

liver and other tissue damage due to granulomas around eggs released by female worms circulating in conjugal pairs with males in the mesenteric bloodsteam 

Trematodes (flukes)

Ascaris lumbricoides

giant roundworm, eggs from feces contaminated soil or food; "worm balls"

Nematodes (roundworms)

Enterobius vermicularis

pinworm, anal to oral via eggs; puritis ani

Nematodes (roundworms)

Necator americanus

(and Ancylostoma duodenale) - hookworm, penetration through skin (e.g. toes)

Nematodes (roundworms)

Dracunculus medinensis 

Guinea worm; ingestion of water with infected copepods; the Caduceus

Nematodes (roundworms)

Procaryotes

(lack a nucleus, mitochondria, endoplasmic reticula, Golgi, lysosomes, division by mitosis and meiosis, and other characteristics common in eucaryotic organisms;

usually a single circular chromosome (nucleoid),

unique 70S ribosomes,

unique cell wall,

motility by flagella that rotate or by endoflagella (axial filaments) in spirochetes,

often have extrachromosomal genetic elements called

plasmids,

and commonly divide by binary fission).

All of the following are different types of bacteria.

Rickettsias and Chlamydias

small Gram negative,

obligately intracellular bacteria

either arthopod borne (Rickettsias) or transmitted by contact (Chlamydias) 

Rickettsia rlckettsii 

Rocky mountain sported fever, wood and dog ticks

procaryotes 

Chlamydia trachomatis 

different serovars cause

(1) nongonococcal urethritis (NOU, a very common STD; females commonly asymptomatic, but may get salpingitis & PID) and inclusion conjunctivitis in infants born by these mothers;

(2) trachoma of the eye (#1 preventable cause of blindness); and

(3) lymphogranuloma venereum (a serious, but uncommon STD)

procaryotes 

Mycoplasmas

wall-less bacteria that are among the smallest of cells; generally animal parasites; "fried egg" colonies on appropriate media

Mycoplasma pneumoniae 

atypical or "walking" pneumonia

Ureaplasma urealyticum 

another cause of NGU

Spirochetes

spiral shaped with flexible walls, move with corkscrew motion by axial filaments

Treponema pallidum

primary (chancre), secondary (rash), and tertiary (gummas, aortic aneurysm, paresis & dementia) syphilis

Spirochetes 

Borrelia burgdorferi

Lyme disease, number one arthropod-borne disease in US; ticks

Spirochetes 

Leptospira interrogans

infectious jaundice (fever, liver and kidney pathology);

urine of infected animals

spirochetes 

Acid-Fast Bacilli

bacteria hard to stain with conventional staining;

once stained resist decolorization with acid-alcohol;

due to high lipid content of wall;

high resistance to antiseptics and disinfectants (next to bacterial endospores);

tuberculin test for TB is an example of a Type IV hypersensitivity reaction

Mycobacterium tuberculosis

TB (granulomas ~ tubercles in lungs); may disseminate -miliary TB

Acid-fast Bacilli

Mycobacterium bovis

TB;

BeG vaccine for TB is an attenuated M bovis; 

pasteurization of milk

Acid-Fast Bacilli

Mycobacterium leprae

Leprosy (Hansen's disease);

Tuberculoid leprosy milder than Leprotamous

Acid-Fast Bacilli

Mycobacterium avium-intracellualre

(MAl) complex-

systemic infection in AIDS and other immunocompromised patients;

very difficult to treat

Acid-fast Bacilli

Obligate Anaerobes

bacteria that will not grow in (and are poisoned by) air; require special incubation conditions (e.g. GasPak or anaerobic glove box)

Clostridium botulinum

botulism (intoxication) and infant botulism (infection, honey); flaccid paralysis.

Obligate Anaerobes.

Gram + spore forming rods

Clostridium perfringens

gas gangrene and food-borne illness

Obligate Anaerobes

Gram + spore forming rods

Clostridium tetani

tetanus ("lock jaw") and neonatal tetanus; spastic paralysis; toxoid vaccine

Obligate Anaerobes.

Gram + spore forming rods

Clostridum difficile

antibiotic associated pseudomembranous colitis

Obligate Anaerobes.

Gram + spore forming rods

Bacteroides fragilis

very prevalent part of normal flora of colon,

often cause mixed infections (e.g. E. coli) when displaced,

intra-abdominal abscesses, pleuropulmonary infections, bacteremia 

Gram-rods 

obligate anaerobes 

Staphylococcus aureus

coagulase +;

a major pathogen producing a spectrum of infections from the localized abscess (pimple, boil) to impetigo to scalded skin syndrome in infants;

toxic shock syndrome associated with tampons;

to osteomyelitis, pneumonia, meningitis, endocarditis, or sepsis with suppuration in any organ;

also major cause of food intoxication;

nosocomial infections; MRSA

Gram+cocci

Staphylococcus epidermidis

CONS;

normal flora of skin, cause infections of implanted catheters and prosthetic devices, nosocomial infections

Gram+ cocci

Staphylococcus saprophyticus

CONS;

normal flora uropathogen that causes about 10 -20% of primary urinary tract infections in young women

gram+ cocci

Streptococcus pyogenes

Gr. A, Bvhemolytic;

causes strep throat and post streptococcal sequelae (acute glomerulonephiritis and rheumatic fever);

scarlet fever, impetigo, cellulitis, puerperal fever, sepsis, acute endocarditis, streptococcal toxic shock syndrome and necrotizing fasciitis ("FEB") with high mortality

Gram+ cocci

Streptococcus agolactiae

Gr B, B-hemolytic; causes neonatal sepsis and meningitis

gram+ cocci

Enterococcus fecalis

Gr. D; causes urinary tract infections and subacute bacterial endocardisis (SBE); nosocomial infections;

a fecal streptococcus in water testing

gram+ cocci

Viridans streptococci

alpha-hemolytic strep of mouth;

cause SSE;

Streptococcus mutans causes dental caries; thick glycocalyx slime produced from dietary sugars -> plaque

gram+ cocci

Streptococcus pneumoniae

alpha-hemolytic;

causes lobar pneumonia, sinusitis, bronchitis, otitis media, and meningitis;

capsule (80+) major virulence factor;

capsular vaccines for pneumonia & otitis media

Gram + cocci

Gram- Cocci

the important ones are fastidious, coffee-bean shaped diplococci, that are oxidase positive;

grow on supplemented chocolate + antimicrobials VCN = Modified Thayer Martin medium

Neisseria gonorrhoeae

gonorrhea, proctitis, salpingitis, pelvic inflammatory disease;

gonococcal bactermia leads to skin lesions, arthritis, and occasionally meningitis;

gonococcal opthalimia neonatorum is infection of the eye of the newborn during passage through infected birth canal (blindness)

gram - cocci

Neisseria meningitidis

meningitis that can be spread human to human;

isolated polysaccharide vaccine

gram- cocci

Bacillus anthrasis

cutaneous anthrax (malignant pustule) & pulmonary anthrax ("woolsorter's disease")

Gram + Aerobic Spore Forming Rods

Bacillus cereus

produces food poisoning of two types (emetic and diarrheal);

eye infections associated with foreign bodies and trauma, and occasional opportunistic infections including endocarditis, meningitis, osteomyelitis and pneumonia

Gram+ Aerobic Spore Forming Rods

Cornebacterium diphtheria

diphtheria; pseudomembrane that may suffocate; toxoid vaccine

gram+ rods

Listeria monocytogenes

meningitis and bacteremia;

granulomatosis infantseptica can result in intrauterine sepsis and death, or development of meningitis

gram+ rods

Salmonella typhi

enteric (typhoid) fever; killed and living attenuated vaccines

Grtam- rods

Salmonella choleraesuis

early bacteremia with focal lesions

Gram- rods

Salmonella enterica (S. enteritidis)

common enterocolitis (gastroenteritis);

many (>2,000) varieties (serotypes, previously designated as different species) based on different 0 and H antigens

Gram - rods

Shigella sonnei

bacillary dysentery (blood and pus from colonic damage), most common cause

gram - rods

Shigella dysenteriae

bacillary dysentery, most severe;

produces Shiga toxin can lead to HUS

gram - rods

Shigella dysenteriae

bacillary dysentery,

most severe; produces Shiga toxin can lead to HUS

Gram - Rods

Escherichia coli

most common cause of urinary tract infections (UTI),

common cause of neonatal meningitis;

septicemia, pneumonia, and meningitis in compromised patients;

nosocomial infections, the fecal coliform; as an enteropathogen as follows:

ETEC- traveler's diarrhea; infantile diarrhea in developing countries; plasmid STILT; LT acts like CT

EHEC- colitis & bloody diarrhea; Shiga-like toxin; hemolytic uremic syndrome (HUS); 0157:H7

Gram - Rods

ETEC

traveler's diarrhea; infantile diarrhea in developing countries; plasmid STILT; LT acts like CT

Gram - Rods

EHEC

colitis & bloody diarrhea; Shiga-like toxin; hemolytic uremic syndrome (HUS); 0157:H7

Gram - Rods

Kledsiella pneumoniae

severe pneumonia, UTI, nosocomial infections; slimy mucoid colonies; coliform

G- Rods

Enterobacter

UTI, nosocomial infections; coliform

G- Rods

Serratia

nosocomial infections

G- Rods

Proteus mirabilis

UTI, infection related kidney stones- urease; nosocomial infections; "swarming"

G- Rods

Vibrio cholerae

cholera; acute explosive diarrhea; killed vaccine (+1-B subunit of CT)

Gram - Rods

Vibrio parahemolyticus

halophilic, acute gastroenteritis due to contaminated raw or partially cooked seafood

Gram - Rods

Vibrio vulnificus

halophilic, severe skin lesions; enteritis (e.g. raw oysters); bacteremia, and death

Gram - Rods

Campylocacter jejuni

microaerophile; diarrhea and dysentery (resembles shigellosis)

Gram - Rods

Helicobacter pylori

microaerophile; gastritis, duodenal and gastric ulcers, gastric cancer

Gram - Rods

Pseudomonas aeruginosa

infections of wounds and burns, respiratory infections in cystic fibrosis patients, nosocomial infections; "blue pus" due to pyocyanin; Exotoxin A acts like diphtheria toxin

Gram - Rods

Yersisnia pestis

bubonic and pneumonic plague; rat flea

G- Rods

Yersinia enterocolitica

food-borne diarrheal illness; severe abdominal pain resembles appendicitis

G- Rods

Francisella tularensis

tularemia, through skin (inflammatory, ulcerating papule) via contact with rabbits, or inhalation (peribronchial inflammation and localized pneumonitis)

G- Rods

Pateurella multocida

human wound infections by bites from cats and dogs

G- Rods

Brucella (B. abortus)

infection of the RES; undulant fever; destroyed in milk by pasteurization

G- Rods

Haemophilus lafluenzae

meningitis in children, occasional respiratory infections; capsule vaccine (HIB)

G- Rods

Bordatella pertussis

whooping cough (pertussis); vaccines old-killed cells, new- toxoid + adhesins

G- Rods

Legionella pneumophila

severe pneumonia (Legionnaires' disease), and Pontiac fever (less severe disease); aerosolized contaminated water

G- Rods

Streptobacillus moniliformis

rat-bite fever

G- Rods

Acellular Microbes

(i.e. lack cellular structures commonly found in eucaryotic andlor prokaryotic organisms); no autonomous metabolism or replication; "alive" only when inside of cells.

Viruses

Viruses

have only one type of nucleic acid (DNA or RNA genome) surrounded by protein capsid composed of capsomeres; some are enveloped; small, filter passing, obligate intracellular parasites of plants, animals, fungi, protists, and bacteria. 

MMR (attenuated measles, mumps, and rubella viruses)

virus

(germ measles) congenital infection in first trimester leads to birth defects; thus, vaccine protects "those yet to born"

virus

vaccine: inactivated (Salk) [attenuated (sabin)]

virus

seasonal vaccine varies changes in hemagglutinin (H) and neuraminidase (N)

virus

virus vaccine avalaible

varicella-zoster

virus 

a vaccine for rabies (and anthrax) was originally produced by Pasteur

(human papilloma virus); cervical cancer

virus; vaccine avalaible

(variola virus) disease eliminated through immunization with cowpox (vaccina virus)

virus, vaccine available 

most common cause of gastroenteritis; all ages but most sever in children

virus- vaccine available 

"Cold sores, fever blisters"

(herpes simplex labialis) - common; Herpes simplex virus type I (HSV 1)

virus, no vaccine

Genital herpes

Herpes simplex virus type 2 (HSV2); also HSVI with oral sex; both HSV 1& 2 latent

virus, no vaccine

rhinovirus, adenovirus, coronaviruses 

virus, no vaccine

rotavirus, Norwalk virus, calciviruses

virus, no vaccine

(rubella, cytomegalovirus, herpes simplex, varicella zoster, herpes B, measles, mumps, some enteroviruses

virus no vaccine

Epstein-Barr [EB] virus

"mono"

virus, no vaccine

(dengue, Hantaan, Junin, Machupo, Lassa fever, Marburg, Ebola Viruses

virus, no vaccine

Prions

infectious proteins (no nucleic acids); associated with slow degenerative diseases of the central nervous system of animals and humans.

Symptoms are loss of muscle control, shivering tremors, dementia, and death.

Vacuolation of neurons and amyloid-like plaque. Spongioform encephalopathies.

Abnormal prion converts normal prion (alpha-helix) to abnormal (beta-pleated sheet). Highly resistant.

Bovine spongioform encephalopathy

mad cow" disease

prion

Scrapie

sheep and goats scrape and rub skin

prion

Creutzfeldt-Jakob diseas

humans; variant (vCJD)- humans consuming meat from SSE animals

Prion

Kuru

associated with ritualistic cannibalism by humans in New Guinea

Prion