USMLE Microbiology Syllabus

Microbiology syllabus — full chapter and topic list

Expand any chapter to see its topics and sub-topics. This is the whole examinable outline for Microbiology in USMLE, not a summary of it.

1. 1

   Bacteriology

   3 topics

   • Gram-positive bacteria
   • Gram-negative bacteria
   • Mycobacteria
2. 2

   Virology

   3 topics

   • DNA viruses
   • RNA viruses
   • Retroviruses
3. 3

   Mycology

   2 topics

   • Yeast infections
   • Mold infections

Microbiology flashcards for USMLE

24 of 50 cards from the Microbiology deck — real questions with worked answers.

1. Which stain distinguishes Gram-positive from Gram-negative bacteria, and what color does each retain?

   The Gram stain: Gram-positive bacteria retain the crystal violet–iodine complex and appear purple/blue (thick peptidoglycan wall); Gram-negative bacteria lose it after alcohol decolorization, take up safranin, and appear pink/red.

2. What are the two main catalase-positive Gram-positive cocci genera, and how are they told apart?

   Staphylococcus (catalase-positive) forms grape-like clusters; Streptococcus (catalase-negative) forms chains/pairs. Among staphylococci, coagulase separates S. aureus (coagulase-positive) from S. epidermidis and S. saprophyticus (coagulase-negative).

3. How are streptococci classified by hemolysis on blood agar?

   Alpha-hemolytic (partial, green): S. pneumoniae, viridans streptococci. Beta-hemolytic (complete, clear): S. pyogenes (Group A), S. agalactiae (Group B). Gamma-hemolytic (none): Enterococcus, some non-enterococcal group D strep.

4. What tests differentiate the major alpha- and beta-hemolytic streptococci?

   Alpha: S. pneumoniae is optochin-sensitive and bile-soluble; viridans are optochin-resistant and bile-insoluble. Beta: S. pyogenes is bacitracin-sensitive (PYR+); S. agalactiae is bacitracin-resistant and hippurate/CAMP test positive.

5. Which toxin causes diphtheria, and what is its mechanism?

   Corynebacterium diphtheriae produces diphtheria exotoxin, which ADP-ribosylates elongation factor 2 (EF-2), halting host protein synthesis. It is encoded by a lysogenic (beta) bacteriophage.

6. What is the key morphological/spore feature and disease association of Bacillus anthracis versus Clostridium species?

   Both are Gram-positive, spore-forming rods. Bacillus is aerobic (B. anthracis causes anthrax, has a polypeptide D-glutamate capsule); Clostridium is anaerobic (C. tetani, C. botulinum, C. perfringens, C. difficile).

7. Compare the mechanisms of tetanus and botulinum toxins.

   Both are protease toxins cleaving SNARE proteins. Tetanospasmin (C. tetani) blocks release of inhibitory GABA/glycine in Renshaw cells causing spastic paralysis; botulinum toxin (C. botulinum) blocks acetylcholine release at the NMJ causing flaccid paralysis.

8. What organism causes Listeriosis, and what are its distinctive features?

   Listeria monocytogenes: a Gram-positive rod that is the only one with an endotoxin-like LPS, shows tumbling motility and actin-based 'rocket' intracellular motility, and grows at cold (4 degrees C, 'cold enrichment'). Causes neonatal meningitis and infection in pregnancy/immunocompromised.

9. Which Gram-positive organisms are the classic causes of nosocomial catheter/prosthetic device infections and UTIs in young women?

   Staphylococcus epidermidis (biofilm on catheters/prosthetics; novobiocin-sensitive) and Staphylococcus saprophyticus (second most common cause of uncomplicated UTI in sexually active young women; novobiocin-resistant).

10. What is the mechanism of the Gram-negative outer membrane endotoxin, and which component is responsible?

    Lipopolysaccharide (LPS) in the outer membrane; its Lipid A component triggers macrophage TLR4/CD14 activation, releasing IL-1, IL-6, and TNF-alpha, causing fever, hypotension, and DIC (septic shock). Endotoxin is heat-stable and not secreted.

11. Which lactose-fermenting Gram-negative rods appear pink on MacConkey agar, and which key ones do not?

    Lactose fermenters (pink): Klebsiella, E. coli, Enterobacter, Citrobacter, Serratia (slow). Non-fermenters (colorless): Shigella, Salmonella, Proteus, Pseudomonas (oxidase-positive).

12. What are the major virulence antigens used to classify enteric Gram-negative bacteria?

    O antigen (outer membrane LPS polysaccharide), H antigen (flagellar protein), and K antigen (capsular polysaccharide). E.g., E. coli O157:H7.

13. How is Pseudomonas aeruginosa characterized, and what is its signature toxin?

    An aerobic, oxidase-positive, non-lactose-fermenting Gram-negative rod producing blue-green pigment (pyocyanin) and a grape-like odor. Exotoxin A inactivates EF-2 (like diphtheria toxin). Causes infections in burns, cystic fibrosis, and immunocompromised hosts.

14. What organism causes cholera, and by what mechanism does it produce watery diarrhea?

    Vibrio cholerae (comma-shaped, oxidase-positive Gram-negative rod). Cholera toxin permanently activates Gs via ADP-ribosylation, increasing adenylate cyclase and cAMP, driving chloride and water secretion into the gut ('rice-water' stools).

15. What are the two urease-positive Gram-negative organisms of major clinical importance, and their consequences?

    Proteus mirabilis (urease raises urine pH, forming struvite kidney stones and 'swarming' motility) and Helicobacter pylori (urease neutralizes stomach acid; causes gastritis, peptic ulcers, and gastric adenocarcinoma/MALT lymphoma).

16. Which Gram-negative organism requires chocolate agar with factors V (NAD) and X (hematin) for growth?

    Haemophilus influenzae. The type b (Hib) capsular polysaccharide (polyribosylribitol phosphate) is the basis of the conjugate vaccine and causes epiglottitis and meningitis.

17. Describe the acid-fast staining property of Mycobacteria and its cause.

    Mycobacteria are acid-fast: they retain carbolfuchsin (Ziehl-Neelsen/Kinyoun stain) after acid-alcohol wash because their cell wall is rich in mycolic acids (long-chain fatty acids), which also make them resist standard Gram staining.

18. What is the classic natural history of Mycobacterium tuberculosis infection, including the Ghon complex?

    Primary TB forms a Ghon focus (subpleural granuloma) plus hilar node involvement = Ghon complex, healing to a Ranke complex. It causes caseating (central necrosis) granulomas via a Th1/CD4 response. Reactivation typically involves the lung apices (high oxygen).

19. What are the primary anti-tuberculosis drugs (RIPE) and one signature toxicity of each?

    Rifampin (orange body fluids, CYP450 induction), Isoniazid (peripheral neuropathy from B6 depletion, hepatotoxicity), Pyrazinamide (hyperuricemia), Ethambutol (optic neuritis/red-green color blindness).

20. Compare tuberculoid and lepromatous leprosy caused by Mycobacterium leprae.

    Tuberculoid (paucibacillary): strong Th1/cell-mediated response, few bacilli, limited hypopigmented skin plaques, better prognosis. Lepromatous (multibacillary): weak Th2 response, high bacterial load, symmetric diffuse skin lesions with leonine facies, worse prognosis. M. leprae prefers cool sites and grows in armadillos.

21. Which Mycobacterium causes disseminated disease in advanced AIDS, and at what CD4 count is prophylaxis indicated?

    Mycobacterium avium-intracellulare (MAC) causes disseminated infection when CD4 counts fall below 50 cells/microliter; azithromycin prophylaxis is given. Treatment uses a macrolide plus ethambutol +/- rifabutin.

22. State the general rule distinguishing DNA viruses from RNA viruses regarding replication site and genome.

    Most DNA viruses replicate in the nucleus (exception: poxviruses, in cytoplasm) and are double-stranded (exception: parvovirus, ssDNA). Most RNA viruses replicate in the cytoplasm (exceptions: influenza and retroviruses use the nucleus) and are single-stranded (exception: reovirus, dsRNA).

23. List the seven families of DNA viruses (mnemonic 'HHAPPPPy').

    Hepadnavirus, Herpesvirus, Adenovirus, Poxvirus, Parvovirus, Papillomavirus, and Polyomavirus. All are double-stranded except Parvovirus (ssDNA), and all are enveloped except Papilloma, Polyoma, Adeno, and Parvo (naked).

24. Which DNA virus is the only single-stranded one, and what diseases does it cause?

    Parvovirus B19 (ssDNA, naked). It causes erythema infectiosum (fifth disease, 'slapped-cheek' rash) in children, aplastic crisis in sickle cell disease, and hydrops fetalis if it infects a fetus by targeting erythroid precursors.

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