Gram-negativeBacilliAnaerobes

Bacteroides fragilis

Encapsulated obligate anaerobic Gram-negative bacillus that is the most common anaerobic pathogen in humans, causing intra-abdominal abscesses, peritonitis, and bacteremia.

Organism Card

DomainMust know
Identity
  • G−ve obligate anaerobic rod [1][2]
  • Bacteroidaceae family; non-spore-forming
  • Most clinically important anaerobe from the GI tract
  • Normal flora of oral cavity and GI tract [1]
Lab discriminator
  • Strict anaerobe: requires anaerobic culture (anaerobic jar / chamber)
  • Growth on Bacteroides bile esculin (BBE) agar: bile-resistant (20% bile), esculin-hydrolysing
  • Catalase +ve (unusual for anaerobes); indole −ve
  • vs Fusobacterium: fusiform morphology, causes Lemierre's disease [1]
  • vs Clostridium: Clostridia are G+ve spore-forming anaerobes
Reservoir / transmission
  • GI tract coloniser — most abundant anaerobe in colonic flora [1]
  • Endogenous infection: breaches gut barrier → contiguous / haematogenous spread
  • No person-to-person transmission of clinical significance
  • Contamination from bowel perforation, surgery, or trauma
Key virulence
  • Polysaccharide capsule (capsular polysaccharide complex, esp. PSA) → abscess formation, anti-phagocytic
  • Superoxide dismutase & catalase → aerotolerance, survives brief O₂ exposure
  • Lipopolysaccharide (LPS) — atypical, low endotoxic activity vs Enterobacteriaceae
  • Succinic acid production → inhibits PMN killing
  • β-lactamase production → increasing antimicrobial resistance [1]
Clinical syndromes
  • Complicated intra-abdominal infections (abscess, secondary peritonitis) — often polymicrobial [1][3][4]
  • Liver abscess (ascending biliary infection route — mixed with E. coli, Klebsiella) [5]
  • Secondary bacterial peritonitis: polymicrobial culture ± Bacteroides = think bowel leak (vs monomicrobial SBP) [3]
  • Acute cholangitis bacteriology: listed alongside E. coli, Klebsiella, Enterobacter, Enterococcus [4]
  • Brain abscess (anaerobic component in mixed infection)
  • Aspiration pneumonia / lung abscess (foul-smelling sputum) [6]
  • Pelvic / tubo-ovarian abscess
  • Bacteraemia (anaerobic blood cultures; may → metastatic abscess)
Diagnosis
  • Specimen: pus / abscess fluid / peritoneal fluid / blood (anaerobic bottle)
  • Anaerobic culture is gold standard — transport rapidly in anaerobic transport medium
  • Foul-smelling pus or gas on imaging suggests anaerobic involvement
  • Pitfall: organism dies quickly with O₂ exposure → false-negative if delayed or improper transport
  • Gram stain: pale-staining G−ve rods; may be pleomorphic
Treatment
  • Expert practice tip: consider adding metronidazole in patients with severe intra-abdominal sepsis to cover Bacteroides fragilis [1][2]
  • Metronidazole = drug of choice for anaerobic coverage
  • Alternatives: carbapenems (imipenem, meropenem), β-lactam/β-lactamase inhibitor combos (piperacillin-tazobactam, amoxicillin-clavulanate)
  • Increasing antimicrobial resistance [1]: ↑β-lactamase production → resistant to penicillin, ampicillin, many cephalosporins
  • Intrinsically resistant to aminoglycosides (anaerobes lack O₂-dependent drug uptake)
  • Source control (surgical drainage of abscess / debridement) is essential alongside antibiotics
Prevention
  • Surgical prophylaxis: metronidazole added for colorectal / GI surgery to cover anaerobes
  • Antibiotic prophylaxis for PD patients undergoing colonoscopy with polypectomy: ampicillin + aminoglycoside ± metronidazole [7]
  • No vaccine available
  • Not a notifiable disease
Classic traps
  • Polymicrobial peritoneal culture with Bacteroides → think secondary bacterial peritonitis (bowel perforation), NOT SBP [3]
  • Foul-smelling discharge / gas-forming infection → think anaerobes (Bacteroides or Clostridium)
  • SBP = monomicrobial (E. coli, Klebsiella, Strep); polymicrobial = secondary [3]
  • Don't confuse with Fusobacterium: Fusobacterium → Lemierre's disease (IJV thrombophlebitis) [1]
  • Aminoglycosides have NO activity against anaerobes — common MCQ trap

Exam Intelligence

  1. GC 105 Expert Practice Tip 6: "Consider adding metronidazole in patients with severe intra-abdominal sepsis to cover Bacteroides fragilis" — this exact tip also appears in the Gen Clerk Microbiology Summary as point #6. This is extremely high-yield for MCQs asking about empirical antibiotic coverage in intra-abdominal sepsis [1][2].

  2. GC 105: B. fragilis is specifically highlighted as a "GI tract coloniser often found in complicated intra-abdominal infections" with "increasing antimicrobial resistance" [1]. Expect MCQs testing that B. fragilis is resistant to standard penicillins and cephalosporins but susceptible to metronidazole and carbapenems.

  3. GC 105: Anaerobes are described as "part of polymicrobial infections & abscesses" — B. fragilis is the prototypical anaerobe in mixed intra-abdominal infections. The polymicrobial nature is a key discriminator from SBP (monomicrobial) [1][3].

  4. Acute cholangitis bacteriology (Felix Lai Medicine & Surgery notes): B. fragilis is listed as one of the causative Gram-negative organisms alongside E. coli, Klebsiella, and Enterobacter. Acute cholangitis questions commonly ask for the bacteriology — do not forget the anaerobic component [4].

  5. Secondary vs spontaneous bacterial peritonitis (senior notes): Polymicrobial culture growth (including Bacteroides) is the most important feature distinguishing secondary bacterial peritonitis from SBP. SBP = single organism that translocated; secondary = direct bowel inoculation [3].

  6. Aminoglycosides do not cover anaerobes — aminoglycosides require aerobic electron transport for drug uptake. This is a commonly tested principle and appears in the context of PD peritonitis and intra-abdominal infection antibiotic choices.

  • B. fragilis vs Fusobacterium: Both are G−ve anaerobic rods. Fusobacterium → Lemierre's disease (internal jugular vein thrombophlebitis after pharyngeal infection); B. fragilis → intra-abdominal infections. GC 105 lists both side-by-side [1].
  • SBP vs secondary peritonitis: If a cirrhotic patient's peritoneal fluid grows polymicrobial organisms (especially with anaerobes like Bacteroides), this is secondary peritonitis → look for a surgical cause (perforation) [3]. SBP grows a single organism and is treated medically.
  • Metronidazole vs carbapenems: Metronidazole is the classic drug for anaerobic coverage. Carbapenems (except ertapenem for Pseudomonas) also cover anaerobes but are broader — exam may test why metronidazole is "added" rather than switching to a carbapenem for cost/stewardship reasons.
  • β-lactamase production: B. fragilis produces chromosomal β-lactamases → resistant to ampicillin, penicillin, and most cephalosporins. This contrasts with above-diaphragm anaerobes (e.g. Peptostreptococcus) which are generally penicillin-susceptible.
  • Common wrong answer: Choosing an aminoglycoside to cover B. fragilis — aminoglycosides require oxygen-dependent uptake and have zero activity against obligate anaerobes.

No directly relevant past paper questions specifically testing Bacteroides fragilis as the primary focus were identified in the indexed past paper material. The organism appears in clinical context within senior notes (cholangitis bacteriology, secondary peritonitis, liver abscess microbiology) but no indexed MCQ, SAQ, or minicase stem from the 2016–2025 Fourth Summative papers specifically asks about B. fragilis identification, treatment, or virulence as the central question.

Students should anticipate B. fragilis appearing as part of broader stems on: (1) empirical antibiotic selection for intra-abdominal sepsis, (2) cholangitis bacteriology, or (3) distinguishing SBP from secondary peritonitis (polymicrobial culture).

[1] Lecture slides: GC 105. Medically important microbes what every doctor should know.pdf [2] Senior notes: Gen Clerk Anaes + Microbiology Summary.pdf [3] Senior notes: Block A - Abdominal distension_ ascites and cirrhosis.pdf; MBBS Final MB (Surgery) (Felix PY Lai).pdf (peritonitis section) [4] Senior notes: MBBS Final MB (Medicine) (Felix PY Lai).pdf; MBBS Final MB (Surgery) (Felix PY Lai).pdf (cholangitis bacteriology) [5] Senior notes: Ryan Ho GI.pdf (pyogenic liver abscess section) [6] Senior notes: Ryan Ho Respiratory.pdf [7] Senior notes: Ryan Ho Urogenital.pdf (PD peritonitis antibiotic prophylaxis)

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