Morphology & taxonomy

Spore-forming bacteria (calcium dipicolinate): Bacillus Clostridium (most Clostridium are motile except C. perfringens).

Encapsulated bacteria & fungi (antiphagocytic)

• Streptococcus pneumoniae · Klebsiella pneumoniae · Haemophilus influenzae · Pseudomonas aeruginosa (slime in CF) · Neisseria meningitidis · Cryptococcus neoformans (fungus) · Bordetella pertussis
• Also: E. coli K1 capsule, B. anthracis poly‑D‑glutamate, Salmonella typhi Vi antigen, S. pyogenes hyaluronic acid capsule.

Biofilm producers

S. epidermidis S. mutans S. aureus P. aeruginosa

Pigment production

• P. aeruginosa → blue‑green (pyocyanin, fluorescein)
• Serratia → red
• S. aureus → yellow
• C. diphtheriae → black/gray

Unique morphology / staining

• Metachromatic granules – Corynebacterium
• Lancet‑shaped diplococci – Pneumococcus
• Kidney‑bean diplococci – Neisseria
• Bipolar (“safety pin”) – Yersinia pestis, Pasteurella multocida
• Gull‑wing appearance – Campylobacter

Viral cytopathic hallmarks

Genetic determinants

• Chromosomal – endotoxin
• Plasmid – many toxins, antimicrobial resistance
• Bacteriophage (lysogenic conversion) – toxins: cholera, botulinum, erythrogenic (S. pyogenes), diphtheria, Shiga toxin

Antigenic variation

N. gonorrhoeae (pili), Borrelia recurrentis, Trypanosoma brucei, HIV.

Invasive factors

• Capsules – antiphagocytic
• M protein (Group A Strep) – antiphagocytic
• Protein A (S. aureus) – inhibits opsonization
• Lipoteichoic acid – attachment (Gram‑positives)
• Pili (N. gonorrhoeae) – antiphagocytic

Extracellular enzymes

Humans as only reservoir

M. tuberculosis M. leprae Shigella S. typhi R. prowazekii Group A Strep N. meningitidis / gonorrhoeae C. diphtheriae S. pneumoniae T. pallidum C. trachomatis

Zoonotic (animal → human)

B. anthracis Salmonella (non‑typhi) Leptospira Borrelia Listeria Brucella F. tularensis P. multocida V. vulnificus Yersinia Campylobacter most Rickettsia C. psittaci rabies virus etc.

Arthropod vectors

• Lice – epidemic typhus, relapsing fever, trench fever
• True bugs – Chagas (kissing bugs)
• Mosquitoes – malaria, dengue, encephalitides, yellow fever, filariasis
• Sandflies – leishmaniasis, bartonellosis
• Fleas – plague, endemic typhus
• Ticks – RMSF, Colorado tick fever, Lyme, ehrlichiosis, babesiosis, tularemia, relapsing fever
• Mites – scrub typhus, rickettsialpox

Transmission by ova

Enterobius Ascaris Toxocara Trichuris Echinococcus Taenia solium (others larval).

Not considered contagious (no human‑to‑human)

Nontuberculous mycobacteria (MAC), non‑spore‑forming anaerobes, Legionella, all fungi except dermatophytes.

TORCH (placental crossing)

Toxoplasma Syphilis (T. pallidum) Rubella CMV HSV‑2 HIV Listeria Coxsackie B Polio B19

Respiratory droplet spread

Group A Strep, S. pneumoniae, influenza, N. meningitidis, rubella, M. tuberculosis, measles, B. pertussis, chickenpox, H. influenzae, P. jirovecii, C. diphtheriae, Mycoplasma pneumoniae.

Granuloma‑forming organisms (most intracellular or persistent antigen):

Francisella Listeria Mycobacterium Treponema pallidum Brucella Actinomyces Histoplasma Blastomyces Coccidioides Schistosoma LGV cat scratch

Infections causing intracerebral calcifications

Toxoplasma CMV Cysticercosis Cryptococcus tuberculous meningitis

Special stains

• Silver stains – Legionella (Dieterle), Pneumocystis & fungi (GMS)
• Acid‑fast (Ziehl‑Neelsen/Kinyoun) – Mycobacterium, Nocardia (partial), Cryptosporidium, Isospora, Cyclospora, Microsporidia (oocysts)
• India ink – Cryptococcus (not reliable if negative)
• Calcofluor white – fungi
• Giemsa – blood protozoa (Plasmodium, Babesia, Trypanosoma, Leishmania), Histoplasma in RES cells

Name / special tests

• PPD / Mantoux – TB
• Lepromin – leprosy
• CAMP test – Group B Strep carriers
• Elek test – toxigenic C. diphtheriae
• Weil‑Felix – Rickettsia (Proteus OX antigens)

Unusual growth requirements

• Haemophilus – X (protoporphyrin IX) and V (NAD/NADP)
• Mycoplasma – cholesterol
• Halophiles: S. aureus (high salt), Group D enterococci (6.5% NaCl), Vibrio (NaCl required)
• Cysteine requirement: Francisella, Legionella, Brucella, Pasteurella

Long incubation cultures

M. tuberculosis (and non‑tuberculous except rapid growers), Mycoplasma pneumoniae, systemic fungi (Blastomyces, Histoplasma, Coccidioides).

Prophylactic treatment (contacts)

N. meningitidis M. tuberculosis (recent converter) H. influenzae B (unvaccinated <6y) N. gonorrhoeae T. pallidum Y. pestis neonatal eyes (N. gonorrhoeae, C. trachomatis, T. pallidum)

Vaccines available in U.S.

Toxoids

Tetanus, diphtheria, pertussis toxoid (DTaP).

Subunit vaccines

• Haemophilus (conjugated capsular polysaccharide)
• N. meningitidis (polysaccharide; pediatric conjugated)
• Pneumococcus (polysaccharide 23‑valent; PCV13 conjugated)

Recombinant

• Hepatitis B (HBsAg in yeast)
• HPV (4 capsid proteins)

• Bacillus anthracis – non‑motile, capsule (poly‑D‑glutamate), zoonotic.
• Clostridium perfringens – non‑motile, lecithinase, collagenase.
• Lysogenic conversion toxins – cholera, botulinum, erythrogenic, diphtheria, Shiga.
• Biofilms – S. epidermidis (catheters), S. mutans (dental), P. aeruginosa (CF).
• Intracellular escape – Listeria, Francisella, Legionella; obligate includes Chlamydia, Rickettsia.

💡 USMLE focus capsular organisms, intracellular pathogens, vaccine types, arthropod vectors, and granulomatous infections.