STEPTRACKERMICROBIOLOGY + GYNECOLOGY + CARDIOLOGY | ANAEROBES & OTHERS | HIGH-YIELD REVIEW

Anaerobes & Other Gram-Negatives

Gut and mouth anaerobes that make foul-smelling abscesses, the vaginal overgrowth behind clue cells, and the slow-growing HACEK group that hides in heart valves.

FOCUS ON
Anaerobes lack catalase/superoxide dismutase, smell foul, form gas and abscesses, and live above the diaphragm (oral: Fusobacterium, Prevotella, Peptostreptococcus) or below it (Bacteroides fragilis, most common anaerobe in intra-abdominal abscess). Aminoglycosides don't work (need O₂ for uptake). Treat with metronidazole, β-lactam/β-lactamase inhibitor, carbapenem; clindamycin above the diaphragm. Gardnerella bacterial vaginosis: thin gray discharge, fishy KOH whiff test, clue cells, pH > 4.5 → metronidazole. HACEK: culture-negative endocarditis.
ORGANISM
FEATURES · VIRULENCE
DISEASE
CLUE · TREATMENT
Bacteroides fragilis
Gram ⁻ rod, capsule (promotes abscess), β-lactamase ⁺; colon flora
Intra-abdominal abscess after bowel perforation or surgery, peritonitis
Metronidazole, piperacillin-tazobactam, carbapenem
Fusobacterium necrophorum
Oral anaerobe
Lemierre syndrome: pharyngitis → septic thrombophlebitis of internal jugular vein → septic lung emboli
Teen with sore throat then neck swelling and lung nodules
Oral anaerobes (Prevotella, Peptostreptococcus, Fusobacterium)
Aspirated with oral secretions
Aspiration pneumonia → lung abscess (posterior segment RUL, superior RLL), empyema
Alcoholism, seizures, poor dentition · ampicillin-sulbactam or clindamycin
Polymicrobial infections
Aerobe uses O₂ → creates anaerobic niche
Diabetic foot ulcers, necrotizing fasciitis (type I), brain abscess
Broad coverage incl. anaerobes
Gardnerella vaginalis
Gram-variable rod; overgrowth as lactobacilli fall (not an STI per se)
Bacterial vaginosis: thin gray-white discharge, fishy odor, little inflammation
Clue cells (epithelial cells coated with bacteria), ⁺ whiff test, pH > 4.5 · metronidazole or clindamycin
Klebsiella granulomatis
Intracellular; tropical regions
Granuloma inguinale (donovanosis): painless beefy-red ulcer, bleeds easily, no nodes
Donovan bodies in macrophages · azithromycin
HACEK group
Haemophilus (parainfluenzae), Aggregatibacter, Cardiobacterium, Eikenella, Kingella — fastidious, oral flora
Culture-negative (slow-growing) subacute endocarditis, large vegetations
Ceftriaxone
Eikenella corrodens
Human mouth flora
Human bite and "clenched-fist" injuries
Amoxicillin-clavulanate
Kingella kingae
Oropharynx of toddlers
Septic arthritis, osteomyelitis in children < 4 years
Hard to culture — PCR
Aggregatibacter actinomycetemcomitans
Oral flora
Aggressive periodontitis, endocarditis
—
Culture-negative endocarditis — others
Prior antibiotics or fastidious organisms
Coxiella, Bartonella, Brucella, HACEK, Tropheryma whipplei
Serology, PCR of valve

Mechanism — why anaerobes resist aminoglycosides

No catalase / SODO₂ is toxic
→
Live where O₂ is absentAbscesses, necrotic tissue
→
Aminoglycoside uptake needs O₂
→
Aminoglycosides useless

Vaginitis compared

CAUSE
DISCHARGE
pH · TEST
TREAT
Bacterial vaginosis
Thin gray, fishy
> 4.5 · clue cells
Metronidazole
Trichomonas
Frothy yellow-green, itchy; strawberry cervix
> 4.5 · motile trophozoites
Metronidazole (treat partner)
Candida
Thick white, cottage cheese
Normal (≤ 4.5) · pseudohyphae
Fluconazole

How it's tested

COMMON CONFUSIONLung abscess from aspiration (oral anaerobes; dependent segments) vs Staph aureus or Klebsiella necrotizing pneumonia (cavities after influenza or in alcoholics).
THE TRAPClindamycin covers anaerobes above the diaphragm, but B fragilis resistance is common — use metronidazole below it.
YOUR APPROACHFoul odor, gas, abscess → anaerobe → site (above vs below diaphragm) → drug that covers it. Culture-negative endocarditis → HACEK or the zoonoses.

If you see… think…

Abscess after appendix rupture, foul smell → Bacteroides fragilis
Sore throat → jugular vein thrombosis → lung nodules → Lemierre (Fusobacterium)
Alcoholic with cavity in the superior segment of RLL → aspiration lung abscess
Thin gray discharge, fishy odor, clue cells → bacterial vaginosis (Gardnerella)
Painless, beefy-red, bleeding genital ulcer → granuloma inguinale
Endocarditis with negative cultures in a patient with poor dentition → HACEK
Hand infection after punching someone in the mouth → Eikenella
Toddler with septic hip, culture negative → Kingella kingae
Anaerobes are naturally resistant to → aminoglycosides
Drug of choice below the diaphragm → metronidazole