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USMLE Step 1 Microbiology: High-Yield Bacteria, Viruses and Fungi (University)

42 cards · 11 topics · by Quizcard team · 0 hearts · Updated 2026-11-04

Gram-positive cocciGram-positive rods (Clostridia)Gram-positive rodsGram-negative cocci (Neisseria)GI gram-negative rodsOther gram-negative rodsAtypical/acid-fast bacteriaSpirochetesAtypical/intracellular organismsVirusesFungi
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Gram-positive cocci

Buzzwords: boils/abscesses with golden pus, toxic shock after tampon use, food poisoning with rapid-onset vomiting from preformed toxin

Answer: Staphylococcus aureus — catalase+, coagulase+, beta-hemolytic clusters on Gram stain; Rx: nafcillin/oxacillin (MSSA) or vancomycin (MRSA).

Explanation

Coagulase distinguishes S. aureus from other staph species; TSST-1 causes toxic shock.

Buzzwords: prosthetic joint/heart valve infection, IV catheter infection, biofilm former

Answer: Staphylococcus epidermidis — coagulase-negative, catalase+, novobiocin sensitive; Rx: vancomycin (often with device removal).

Explanation

Biofilm production on foreign material is its hallmark virulence mechanism.

Buzzwords: pharyngitis that can progress to rheumatic fever, scarlet fever with sandpaper rash, necrotizing fasciitis

Answer: Streptococcus pyogenes (Group A Strep) — catalase-negative, beta-hemolytic, bacitracin sensitive; Rx: penicillin G.

Explanation

Rheumatic fever and glomerulonephritis are post-strep sequelae, not direct infections.

Buzzwords: rusty-colored sputum, most common cause of adult meningitis and otitis media

Answer: Streptococcus pneumoniae — catalase-negative, alpha-hemolytic, optochin sensitive, bile soluble, encapsulated diplococci; Rx: penicillin/amoxicillin or ceftriaxone.

Explanation

Capsule is the main virulence factor; vaccines target capsular polysaccharides.

Buzzwords: UTI or endocarditis in elderly after GI/GU procedure, vancomycin-resistant in hospitals

Answer: Enterococcus faecalis/faecium — catalase-negative, grows in bile and 6.5% NaCl; Rx: ampicillin ± gentamicin, or linezolid/daptomycin for VRE.

Explanation

More resistant than Streptococcus; often tested for its resilience and hospital-acquired VRE.

Gram-positive rods (Clostridia)

Buzzwords: watery diarrhea or pseudomembranous colitis after clindamycin/antibiotic use

Answer: Clostridioides difficile — gram-positive anaerobic rod, toxin A/B stool assay; Rx: oral vancomycin or fidaxomicin, stop offending antibiotic.

Explanation

Disrupts normal gut flora, allowing overgrowth and toxin-mediated colitis.

Buzzwords: lockjaw, risus sardonicus, muscle rigidity after a rusty nail wound

Answer: Clostridium tetani — gram-positive anaerobic rod; tetanospasmin blocks glycine/GABA release; Rx: metronidazole + tetanus immune globulin + vaccine.

Explanation

Blocking inhibitory neurotransmitters causes unopposed muscle contraction.

Buzzwords: floppy baby after honey ingestion, descending flaccid paralysis

Answer: Clostridium botulinum — gram-positive anaerobic rod; toxin blocks ACh release at the neuromuscular junction; Rx: botulism immune globulin (antitoxin).

Explanation

Opposite mechanism to tetanus toxin — causes flaccid rather than spastic paralysis.

Buzzwords: gas gangrene with crepitus after trauma, double zone of hemolysis

Answer: Clostridium perfringens — gram-positive anaerobic rod; alpha toxin (lecithinase) destroys cell membranes; Rx: surgical debridement + penicillin.

Explanation

Produces gas in tissue from fermentation, explaining crepitus on exam.

Gram-positive rods

Buzzwords: gray pseudomembrane in the pharynx, bull neck, myocarditis

Answer: Corynebacterium diphtheriae — gram-positive club-shaped rods with metachromatic granules, Elek test for toxin; Rx: antitoxin + erythromycin/penicillin.

Explanation

Diphtheria toxin inhibits elongation factor-2, halting protein synthesis.

Buzzwords: meningitis in neonates, elderly, or pregnant women from unpasteurized dairy/deli meats

Answer: Listeria monocytogenes — gram-positive rod, beta-hemolytic, tumbling motility at room temperature; Rx: ampicillin.

Explanation

Facultative intracellular organism that spreads cell-to-cell via actin rockets.

Buzzwords: painless black eschar (cutaneous), woolsorter's disease (pulmonary), bioterrorism agent

Answer: Bacillus anthracis — gram-positive spore-forming rod, boxcar-shaped chains; Rx: ciprofloxacin or doxycycline.

Explanation

Spores can be inhaled, ingested, or inoculated through skin, giving three clinical forms.

Gram-negative cocci (Neisseria)

Buzzwords: petechial rash with meningitis in a college dorm or military recruit, Waterhouse-Friderichsen

Answer: Neisseria meningitidis — gram-negative diplococci, oxidase positive, ferments maltose; Rx: ceftriaxone; prophylaxis with rifampin/ciprofloxacin for contacts.

Explanation

Adrenal hemorrhage (Waterhouse-Friderichsen) causes acute adrenal insufficiency.

Buzzwords: purulent urethral discharge, septic arthritis in a sexually active young adult, neonatal conjunctivitis

Answer: Neisseria gonorrhoeae — gram-negative diplococci, oxidase positive, does not ferment maltose; Rx: ceftriaxone + azithromycin/doxycycline to cover chlamydia.

Explanation

No capsule or effective vaccine due to antigenic variation of pili.

GI gram-negative rods

Buzzwords: bloody diarrhea with hemolytic uremic syndrome after undercooked beef

Answer: EHEC (E. coli O157:H7) — produces Shiga-like toxin, non-invasive; supportive care only — avoid antibiotics (increase HUS risk).

Explanation

Toxin inhibits the 60S ribosomal subunit, same mechanism as Shigella toxin.

Buzzwords: traveler's diarrhea, watery, no blood or pus

Answer: ETEC — produces heat-labile (increases cAMP) and heat-stable (increases cGMP) toxins; Rx: supportive, fluoroquinolone/azithromycin if severe.

Explanation

Heat-labile toxin mimics cholera toxin mechanism via Gs activation.

Compare Salmonella vs Shigella: motility, H2S production, infectious dose

Answer: Salmonella: motile, H2S+, high infectious dose, can bacteremia. Shigella: non-motile, H2S-, very low infectious dose, spreads person-to-person via Shiga toxin. Both cause bloody diarrhea; Rx supportive ± fluoroquinolone/azithromycin.

Explanation

Shigella invades via M cells and spreads cell-to-cell by actin polymerization, similar to Listeria.

Other gram-negative rods

Buzzwords: burn wound infection, hot tub folliculitis, ecthyma gangrenosum, blue-green pigment with grape odor

Answer: Pseudomonas aeruginosa — gram-negative rod, oxidase positive, pyocyanin pigment; Rx: antipseudomonal penicillin (piperacillin) + aminoglycoside, or cefepime/ciprofloxacin.

Explanation

Common in cystic fibrosis, burn patients, and ventilator-associated pneumonia.

Buzzwords: currant-jelly sputum, aspiration pneumonia in an alcoholic or diabetic

Answer: Klebsiella pneumoniae — gram-negative encapsulated lactose-fermenting rod; Rx: 3rd-generation cephalosporin (ceftriaxone).

Explanation

Thick capsule produces the viscous, blood-tinged sputum.

Buzzwords: peptic ulcer disease, gastric MALT lymphoma, urease positive organism

Answer: Helicobacter pylori — gram-negative curved rod, urease positive (urea breath test); Rx: PPI + amoxicillin + clarithromycin (triple therapy).

Explanation

Urease neutralizes stomach acid, allowing survival in the gastric mucosa.

Buzzwords: rice-water stool, severe dehydration after contaminated water

Answer: Vibrio cholerae — comma-shaped gram-negative rod, grows on alkaline media; cholera toxin permanently activates Gs/adenylate cyclase; Rx: oral rehydration ± doxycycline.

Explanation

Massive cAMP increase drives Cl- secretion and profuse watery diarrhea.

Buzzwords: atypical pneumonia with GI symptoms and hyponatremia, linked to AC units/water towers

Answer: Legionella pneumophila — gram-negative rod, silver stain, grows on charcoal yeast extract with cysteine/iron, detected by urine antigen; Rx: azithromycin or fluoroquinolone.

Explanation

Does not spread person-to-person; acquired from aerosolized water sources.

Buzzwords: whooping cough with inspiratory whoop in an unvaccinated child, lymphocytosis

Answer: Bordetella pertussis — gram-negative coccobacillus, pertussis toxin disables inhibitory Gi protein; Rx: azithromycin (macrolide).

Explanation

Toxin increases cAMP in immune cells, impairing chemotaxis.

Buzzwords: epiglottitis or meningitis in an unvaccinated child, requires special growth factors

Answer: Haemophilus influenzae — gram-negative coccobacillus requiring factor V (NAD) and X (hematin); type b capsule most virulent; Rx: ceftriaxone; prevented by Hib vaccine.

Explanation

Grows on chocolate agar, which supplies the needed growth factors.

Atypical/acid-fast bacteria

Buzzwords: chronic cough, night sweats, weight loss, caseating granulomas

Answer: Mycobacterium tuberculosis — acid-fast rod (mycolic acid cell wall), Ziehl-Neelsen stain; Rx: RIPE regimen (rifampin, isoniazid, pyrazinamide, ethambutol).

Explanation

Forms Ghon complex/caseating granulomas; reactivation occurs with immunosuppression.

Spirochetes

Buzzwords: painless genital chancre, palmar/plantar rash, later tabes dorsalis or gummas

Answer: Treponema pallidum (syphilis) — spirochete seen by dark-field microscopy; screen with VDRL/RPR, confirm with FTA-ABS; Rx: penicillin G.

Explanation

Primary, secondary, and tertiary stages represent progressive disease over years.

Buzzwords: bullseye erythema migrans rash after an Ixodes tick bite, later arthritis or Bell's palsy

Answer: Borrelia burgdorferi (Lyme disease) — spirochete; Rx: doxycycline.

Explanation

Early disseminated disease can cause facial nerve palsy and cardiac block.

Atypical/intracellular organisms

Buzzwords: rash starting on wrists/ankles and spreading centrally after a tick bite in the southeastern US

Answer: Rickettsia rickettsii (Rocky Mountain spotted fever) — obligate intracellular organism infecting endothelial cells; Rx: doxycycline.

Explanation

Vasculitis from endothelial infection explains the rash and potential DIC.

Buzzwords: nongonococcal urethritis, reactive arthritis triad, neonatal conjunctivitis/pneumonia

Answer: Chlamydia trachomatis — obligate intracellular, lacks peptidoglycan, elementary/reticulate body life cycle; Rx: azithromycin or doxycycline.

Explanation

Often co-infects with gonorrhea, hence dual coverage in treatment.

Buzzwords: walking pneumonia in a young adult, patchy CXR worse than physical exam, no cell wall

Answer: Mycoplasma pneumoniae — lacks a cell wall (not Gram stainable), cold agglutinins (IgM), grows on Eaton's agar; Rx: azithromycin or doxycycline (beta-lactams ineffective).

Explanation

Absence of a cell wall explains resistance to penicillins and cephalosporins.

Viruses

Buzzwords: painful grouped vesicles on an erythematous base, cold sores or genital ulcers

Answer: Herpes simplex virus (HSV-1/2) — dsDNA virus, Tzanck smear shows multinucleated giant cells; Rx: acyclovir/valacyclovir.

Explanation

HSV-1 classically oral, HSV-2 genital, though overlap is common.

Buzzwords: chickenpox with vesicles in different stages in a child, shingles in a dermatomal pattern in an adult

Answer: Varicella-zoster virus — dsDNA herpesvirus, latent in dorsal root ganglia; Rx: acyclovir; prevented by varicella/shingles vaccines.

Explanation

Reactivation occurs with age-related or acquired immunosuppression.

Buzzwords: fever, pharyngitis, posterior cervical lymphadenopathy, splenomegaly; amoxicillin causes a rash

Answer: Epstein-Barr virus (mononucleosis) — dsDNA, infects B cells via CD21; heterophile antibody (Monospot) positive; associated with Burkitt lymphoma; Rx: supportive.

Explanation

Atypical reactive T lymphocytes are seen on peripheral smear.

Buzzwords: mono-like illness that is heterophile-negative, congenital 'blueberry muffin' baby, retinitis in AIDS

Answer: Cytomegalovirus — dsDNA herpesvirus, owl's-eye intranuclear inclusions; Rx: ganciclovir.

Explanation

Leading cause of congenital infection and opportunistic retinitis in advanced HIV.

Buzzwords: genital warts, cervical cancer, koilocytes on Pap smear

Answer: Human papillomavirus — dsDNA virus; E6/E7 proteins inactivate p53/Rb; Rx: no cure, Gardasil vaccine for prevention, imiquimod/cryotherapy for warts.

Explanation

Types 6/11 cause warts (low risk), 16/18 cause cancer (high risk).

Buzzwords: abrupt fever, myalgia, and cough in winter; pandemics from antigenic shift

Answer: Influenza virus — segmented negative-sense ssRNA orthomyxovirus with hemagglutinin and neuraminidase; Rx: oseltamivir (neuraminidase inhibitor) within 48 hours.

Explanation

Shift (reassortment) causes pandemics; drift (mutation) causes seasonal epidemics.

Buzzwords: CD4 count under 200 with opportunistic infections

Answer: HIV — positive-sense ssRNA retrovirus, binds CD4 via gp120 plus CCR5/CXCR4 coreceptor; diagnosed by ELISA/Western blot or viral load; Rx: combination antiretroviral therapy (ART).

Explanation

Reverse transcriptase converts RNA genome into DNA for integration into host chromatin.

Interpret hepatitis B serology: HBsAg+, HBeAg+, anti-HBc IgM+

Answer: Acute active infection with high infectivity (HBeAg = active viral replication marker).

Explanation

Recovery shows anti-HBs+ and anti-HBc+; vaccination shows anti-HBs+ alone; chronic infection shows HBsAg+ beyond 6 months.

Fungi

Buzzwords: white curd-like oral or vaginal discharge, pseudohyphae with budding yeast

Answer: Candida albicans — dimorphic fungus, forms germ tubes at 37°C; Rx: fluconazole (topical nystatin for thrush).

Explanation

Common in immunosuppressed patients, diabetics, and after antibiotic use.

Buzzwords: fungus ball in a lung cavity, septate hyphae branching at 45°, invasive pneumonia in immunocompromised

Answer: Aspergillus fumigatus — septate hyphae with acute-angle (45°) branching; causes allergic bronchopulmonary aspergillosis; Rx: voriconazole.

Explanation

Fungus balls (aspergillomas) form in pre-existing lung cavities, e.g., from prior TB.

Buzzwords: meningitis in an AIDS patient, exposure to soil/pigeon droppings, India ink halo

Answer: Cryptococcus neoformans — encapsulated yeast, visualized with India ink stain, latex agglutination detects capsular antigen; Rx: amphotericin B + flucytosine, then fluconazole.

Explanation

Thick polysaccharide capsule is the key virulence factor and diagnostic clue.

Buzzwords: pneumonia-like illness in the Ohio/Mississippi river valley, bat or bird droppings, intracellular yeast in macrophages

Answer: Histoplasma capsulatum — dimorphic fungus, small oval yeast found inside macrophages; Rx: itraconazole (amphotericin B if severe).

Explanation

Classic exposure history is caves or old buildings with bird/bat guano.

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