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High-Yield Microbiology: Bacteria, Viruses & Fungi for the MCAT

Microbiology terrifies most pre-med students because of sheer volume — hundreds of organisms, each with their own virulence factors, treatments, and clinical presentations. This guide collapses all of it into a systematic, high-yield framework built around the organisms that actually appear on exams. Know these cold and microbiology becomes one of your highest-scoring sections.

AI-generated content. This guide was written by MedAI's AI and is intended as a study aid. Always cross-reference with your official course materials, textbooks, and instructor guidance before your exam.

The Master Framework: Gram Stain + Morphology + Oxygen

Every bacterium can be classified by three questions: (1) Gram-positive or Gram-negative? (2) Cocci or bacilli (or spiral)? (3) Aerobe, anaerobe, or facultative? This 3-question tree narrows any unknown organism down to a handful of candidates.

Category	Key Organisms	Classic Diseases
Gram+ cocci	Staph aureus, Staph epidermidis, Strep pyogenes, Strep pneumoniae, Enterococcus	Boils, endocarditis, strep throat, pneumonia, UTI
Gram+ bacilli	Bacillus anthracis, C. difficile, C. perfringens, Listeria, Corynebacterium	Anthrax, pseudomembranous colitis, gas gangrene, neonatal meningitis, diphtheria
Gram− cocci	Neisseria gonorrhoeae, Neisseria meningitidis, Moraxella	Gonorrhea, meningitis, otitis media
Gram− rods (enteric)	E. coli, Salmonella, Shigella, Klebsiella, Pseudomonas, H. pylori, Campylobacter	UTI, typhoid, dysentery, aspiration pneumonia, gastric ulcer, Guillain-Barré
Anaerobes	Bacteroides fragilis, C. difficile, C. perfringens, Actinomyces	Abdominal abscess, colitis, gas gangrene, cervicofacial infection

The Big 10 High-Yield Bacteria

1. Staphylococcus aureus

Gram+ cocci in clusters. Catalase+ and coagulase+ (distinguishes from other staph)
Toxins: TSST-1 (toxic shock syndrome, "superantigen"), protein A (binds IgG Fc), exfoliatin (scalded skin syndrome), Panton-Valentine leukocidin (PVL — necrotizing pneumonia, furuncles)
Diseases: skin infections (cellulitis, furuncles), pneumonia (post-influenza), osteomyelitis (#1 cause), endocarditis (IV drug use), food poisoning (preformed toxin — vomiting within 1–6 hrs)
MRSA: methicillin-resistant due to altered PBP2a (encoded by mecA gene). Treat with vancomycin (or linezolid, daptomycin)

2. Streptococcus pneumoniae

Gram+ diplococci. Alpha-hemolytic (green on blood agar). Optochin-sensitive (distinguishes from Viridans strep)
Encapsulated (polysaccharide capsule — the major virulence factor; resists phagocytosis)
Diseases: "MOPS" — Meningitis, Otitis media, Pneumonia, Sinusitis. #1 cause of each in adults.
Risk: asplenic patients (no spleen to filter encapsulated bacteria) — vaccinate with PPSV23/PCV15/PCV20

3. Neisseria meningitidis

Gram− diplococci. Encapsulated. Uses maltose and glucose (distinguishes from N. gonorrhoeae which uses glucose only)
Spreads in crowded spaces (college dorms, military barracks)
Diseases: bacterial meningitis, Waterhouse-Friderichsen syndrome (bilateral adrenal hemorrhage, septic shock, petechial rash)
Deficiency in C5-C9 (terminal complement) → recurrent Neisseria infections

4. Mycobacterium tuberculosis

Acid-fast (mycolic acid-rich waxy cell wall). Non-gram staining. Slow-growing (doubling time ~24 hrs).
Transmitted via respiratory droplet nuclei. Ghon complex: granuloma in lung + ipsilateral hilar lymphadenopathy.
Primary TB: usually asymptomatic, immune containment. Reactivation TB: apical lung lesion, cavitation, hemoptysis, night sweats, weight loss.
Treatment: RIPE (Rifampin, Isoniazid, Pyrazinamide, Ethambutol) × 2 months, then RI × 4 months.
B6 (pyridoxine) must be given with isoniazid to prevent peripheral neuropathy.

5. E. coli

The most versatile pathogen in medicine. Different pathotypes cause completely different diseases:

E. coli Pathotype	Mechanism	Clinical Disease
ETEC (enterotoxigenic)	Heat-labile (LT) + heat-stable (ST) toxins	Traveler's diarrhea — watery, no blood
EPEC (enteropathogenic)	Attaches and effaces (AE lesion)	Infantile diarrhea in developing countries
EIEC (enteroinvasive)	Invades intestinal epithelium like Shigella	Dysentery (blood/mucus in stool)
EHEC O157:H7	Shiga-like toxin → HUS	Bloody diarrhea → Hemolytic-Uremic Syndrome (HUS)
UPEC (uropathogenic)	Type 1 fimbriae; P fimbriae	#1 cause of UTI; ascending pyelonephritis
Neonatal meningitis	K1 capsule	E. coli is #2 cause of neonatal meningitis (behind GBS)

Viral High-Yield Summary

Virus	Key Features	Disease	Vaccine?
HIV	RNA retrovirus; infects CD4⁺ T cells via gp120-CD4/CCR5; reverse transcriptase → integrase → protease	AIDS: opportunistic infections (PCP, CMV, MAC)	No
Influenza A	Segmented (−) ssRNA; hemagglutinin (HA) and neuraminidase (NA) subtypes; antigenic drift/shift	Flu; secondary bacterial pneumonia (staph)	Yes (annual)
EBV	dsDNA herpesvirus; infects B cells via CD21; heterophile antibodies (+)	Infectious mono, Burkitt lymphoma, nasopharyngeal carcinoma, PTLD	No
CMV	dsDNA herpesvirus; owl-eye inclusions	Mono in immunocompetent; congenital disease; retinitis in AIDS	No
HSV-1/2	dsDNA; latent in dorsal root ganglia	Oral (HSV-1)/genital (HSV-2) herpes; encephalitis (HSV-1 in temporal lobe)	No
HPV 16/18	dsDNA; E6 degrades p53; E7 inactivates Rb	Cervical cancer, anal cancer, oropharyngeal cancer	Yes (Gardasil)
HBV	dsDNA hepadnavirus; HBsAg, HBeAg, anti-HBc markers	Hepatitis B, cirrhosis, HCC	Yes
SARS-CoV-2	Enveloped (+) ssRNA; spike protein binds ACE2	COVID-19: pneumonia, hypercoagulability, MIS-C	Yes (mRNA)

Fungi: The Clinical Pearls

Organism	Morphology	Infection	Key Fact
Candida albicans	Budding yeast + pseudohyphae	Thrush, vaginal candidiasis, esophagitis (AIDS), systemic (ICU)	Germ tube test+ ; treat with fluconazole
Aspergillus fumigatus	Septate hyphae with 45° branching	Allergic bronchopulmonary aspergillosis, invasive (neutropenic)	Galactomannan antigen; treat voriconazole
Cryptococcus neoformans	Encapsulated yeast; India ink positive	Meningitis (AIDS); soap-bubble lesions in brain	Latex agglutination for capsule antigen; treat Amphotericin B + flucytosine
Pneumocystis jirovecii	Fungus (formerly classified as protozoa)	PCP pneumonia (AIDS, CD4 <200)	Silver stain; treat TMP-SMX; prophylax when CD4 <200
Histoplasma capsulatum	Dimorphic (yeast in tissue, mold in soil)	Pulmonary histoplasmosis; Ohio/Mississippi river valleys; bat caves	Macrophage intracellular yeast; urine antigen test

The Dimorphic Fungi Mnemonic

"Dimorphic fungi are Thermal dimorphs: Mold in the Cold, Yeast in the Heat (body temperature)." The key dimorphic fungi: Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, Sporothrix. Exception: Candida is a yeast at BOTH temperatures but forms pseudohyphae.