This page covers anaerobic physiology and classification, clinical syndromes caused by anaerobes, sample collection and transport challenges, laboratory methods for anaerobic culture, and the key clinical organisms with their distinguishing features and clinical significance.
What Are Anaerobes and Why Are They Clinically Important?
Anaerobic organisms cannot use oxygen as a terminal electron acceptor for aerobic respiration. They vary in their oxygen tolerance:
Strict (obligate) anaerobes: cannot survive in the presence of atmospheric oxygen (21 per cent O2). Examples: Bacteroides fragilis, Clostridium perfringens, Fusobacterium necrophorum, Prevotella species, Peptostreptococcus (reclassified into multiple genera).
Aerotolerant anaerobes: can survive in air but grow better anaerobically. Example: Clostridium tertium.
Facultative anaerobes can grow with or without oxygen (E. coli, Staphylococcus): these are not anaerobes.
Microaerophiles: require reduced oxygen concentrations (2 to 10 per cent O2) rather than full anaerobiosis. Example: Helicobacter pylori, Campylobacter.
Anaerobes are the dominant members of the normal human microbiota: they outnumber aerobic organisms in the colon by approximately 1,000 to 1. The anaerobic microbiota of the colon (dominated by Bacteroides, Prevotella, Clostridium, and Fusobacterium) are essential for gut health but become pathogenic when they penetrate tissue barriers through perforation, ischaemia, or trauma.
Clinical Syndromes Caused by Anaerobes
Intra-abdominal sepsis: the most common major anaerobic infection syndrome. Bowel perforation (appendicitis, diverticulitis, perforated peptic ulcer, colon cancer perforation) contaminates the peritoneum with a mixed flora containing hundreds of colonic organisms. The clinically critical pathogens are Bacteroides fragilis (the most virulent anaerobe, the most common cause of anaerobic bacteraemia, resistant to many penicillins through beta-lactamase production) combined with coliforms (E. coli, Klebsiella). Treatment of intra-abdominal sepsis must cover both Bacteroides and coliform components: piperacillin-tazobactam or carbapenems cover both; cephalosporins require addition of metronidazole for Bacteroides coverage.
Aspiration pneumonia and lung abscess: aspiration of oral flora (rich in anaerobes from the gingival crevice) into the lower respiratory tract causes aspiration pneumonia. Lung abscess forms when the infection is contained and causes necrosis of lung parenchyma. The causative organisms are the anaerobes of the gingival flora: Prevotella, Fusobacterium, Peptostreptococcus, and microaerophilic streptococci. Treatment: co-amoxiclav or amoxicillin-metronidazole or clindamycin (historically, though increasing resistance). Prolonged treatment of 4 to 8 weeks is required for lung abscess.
Necrotising soft tissue infections (NSTI): include necrotising fasciitis and gas gangrene (myonecrosis). Gas gangrene is caused by Clostridium perfringens, producing alpha-toxin (a phospholipase) that destroys cell membranes, causing rapid spreading myonecrosis with gas production. Necrotising fasciitis is most commonly polymicrobial (Type I, involving mixed aerobic-anaerobic flora including Bacteroides, Peptostreptococcus, and coliforms) or monomicrobial (Type II, S. pyogenes, the "flesh-eating disease"). Both are surgical emergencies requiring immediate wide excision.
Brain abscess: predominantly caused by the anaerobes of the oral cavity and sinuses: Fusobacterium, Prevotella, Streptococcus milleri group (microaerophilic streptococci: S. anginosus, S. constellatus, S. intermedius — these form purulent foci particularly well, hence the informal name "S. milleri" for this clinically unified group). Brain abscess is almost always polymicrobial. Contiguous spread from ear, sinus, or dental infection is the most common source.
Bacteraemia with Fusobacterium necrophorum (Lemierre's syndrome): Fusobacterium necrophorum is an oral anaerobe that causes Lemierre's syndrome: septic thrombophlebitis of the internal jugular vein following oropharyngeal infection (tonsillitis or peritonsillar abscess), with septic emboli to the lungs and other sites. Primarily affects young adults. The organism is highly susceptible to penicillin and metronidazole. Recognition is important as the condition is life-threatening and frequently missed.
Sample Collection for Anaerobic Culture
Anaerobic organisms die rapidly in the presence of oxygen. Sample collection, transport, and processing must minimise oxygen exposure.
Appropriate samples for anaerobic culture: aspirated abscess pus (aspirated into a syringe, capped, or transferred to anaerobic transport media immediately), tissue biopsy (placed in anaerobic transport medium), blood cultures (inoculated into anaerobic blood culture bottles), body fluids (pleural, peritoneal, joint: aspirated and transported in a syringe or anaerobic transport system).
Samples that should NOT be submitted for anaerobic culture: swabs from any site with normal anaerobic flora (wound swabs from open wounds, perineal swabs, vaginal swabs except for Actinomyces or BV investigation) and urine (anaerobes are not meaningful pathogens in UTI and are present in periurethral flora). These samples cannot be interpreted because of oropharyngeal or perineal anaerobic colonisation.
Transport: anaerobic transport systems (Anaerocult, Port-a-Cul) maintain a reduced oxygen environment. Samples should be plated within 30 minutes to 2 hours ideally. Each hour of delay at room temperature reduces anaerobic yield.
Laboratory Processing: Anaerobic Culture
Specimens are inoculated onto blood agar (with and without antibiotics to suppress normal flora), Bacteroides Bile Esculin (BBE) agar (selective for Bacteroides fragilis group: organisms growing on BBE produce a black precipitate from esculin hydrolysis), and kanamycin-vancomycin laked blood agar (KVLB, selective for gram-negative anaerobes) alongside aerobic plates.
Plates are incubated in an anaerobic cabinet or jar (with hydrogen and CO2 generating sachets to remove oxygen) at 37 degrees Celsius for 48 hours as routine, with extended incubation to 5 to 7 days for suspected Actinomyces or other slow growers.
Identification by MALDI-TOF (with anaerobic database) is now the primary identification method for most anaerobes, replacing laborious biochemical testing.
Frequently Asked Questions
What are anaerobic bacteria?
Anaerobes are bacteria that cannot survive in the presence of atmospheric oxygen or that grow only under reduced oxygen conditions. Strict anaerobes cannot tolerate oxygen at all. They are the dominant organisms in the normal colon, gingival crevice, and vagina.
Why are anaerobes frequently not grown from clinical samples?
Anaerobes require oxygen-free conditions for survival and growth. Poor sample collection (exposed to air), inadequate transport conditions, or failure to use anaerobic culture media and incubation means anaerobes die before reaching the laboratory. This leads to underdiagnosis of anaerobic infection.
What is Bacteroides fragilis and why is it clinically important?
Bacteroides fragilis is the most common anaerobic blood culture isolate and the most clinically significant anaerobic Gram-negative rod. It is the most virulent gut anaerobe, producing a polysaccharide capsule and the B. fragilis toxin (fragilysin, a metalloprotease). It is also inherently resistant to most penicillins through chromosomal beta-lactamase production. Treatment requires metronidazole, piperacillin-tazobactam, carbapenems, or moxifloxacin depending on susceptibility.
What is Lemierre's syndrome?
Lemierre's syndrome is a life-threatening condition caused by Fusobacterium necrophorum, characterised by: oropharyngeal infection (typically tonsillitis), septic thrombophlebitis of the internal jugular vein, bacteraemia, and septic emboli to the lungs and other organs. It predominantly affects previously healthy young adults. It is often called "the forgotten disease" because of diagnostic delays. Treatment with penicillin-based therapy and metronidazole plus anticoagulation for thrombosis.
What is gas gangrene?
Gas gangrene (clostridial myonecrosis) is a rapidly spreading and life-threatening deep soft tissue infection caused by Clostridium perfringens (or other Clostridium species). The organism produces alpha-toxin (phospholipase C) that destroys cell membranes, causing rapid tissue necrosis. Gas is produced in the tissues (visible on X-ray as soft tissue gas). It is a surgical emergency requiring immediate aggressive debridement or amputation, plus penicillin and clindamycin (to inhibit toxin production).
What organisms cause brain abscess?
Brain abscess is nearly always polymicrobial, with anaerobes predominating in most cases. The most common organisms are: Streptococcus milleri group (S. anginosus, S. constellatus, S. intermedius), Prevotella species, Fusobacterium species, Peptostreptococcus species, and co-infecting aerobic organisms (S. aureus in post-traumatic abscesses, gram-negative rods in post-operative cases). Treatment requires prolonged IV antibiotics (often 4 to 8 weeks) and neurosurgical drainage.
Why does intra-abdominal infection treatment require anaerobic cover?
Bowel perforation releases colonic contents into the peritoneum, including Bacteroides fragilis and other anaerobes that are the dominant colonic flora. Without anaerobic coverage (metronidazole, piperacillin-tazobactam, or carbapenems), abscess formation and persistent peritonitis occur even if the aerobic gram-negative component is treated. Adequate surgical source control (drainage, repair, resection) is equally essential.
What is Actinomyces and how is it different from other anaerobes?
Actinomyces israelii and related species are slow-growing, gram-positive, filamentous anaerobes (resembling fungi in morphology but true bacteria). They cause actinomycosis: a chronic, slowly progressive infection characterised by abscess formation, draining sinuses with characteristic yellow "sulphur granules" (colonies of Actinomyces filaments), and woody induration. Classical sites: cervicofacial (jaw after dental extraction or trauma), pulmonary (aspiration), and abdominal (usually post-surgery or in relation to IUDs). Treatment requires prolonged high-dose penicillin (6 to 12 months).
What is the significance of gas on imaging in soft tissue infections?
Gas (air/gas pockets) in soft tissue visible on X-ray, CT, or MRI in the context of a soft tissue infection is a medical emergency. It indicates: anaerobic infection producing gas (clostridial myonecrosis, necrotising fasciitis with mixed flora), or a gas-forming facultative anaerobe. Soft tissue gas in an infected area requires immediate surgical assessment for necrotising soft tissue infection. CT is more sensitive than X-ray for soft tissue gas.
What antibiotics cover anaerobes?
Antibiotics with reliable anaerobic activity: metronidazole (excellent for all gut anaerobes, first choice for Bacteroides and CDI), piperacillin-tazobactam (covers Bacteroides via the tazobactam component), carbapenems (imipenem, meropenem: broadest anaerobic cover), clindamycin (historically widely used for anaerobes including above-diaphragm infections, but increasing Bacteroides resistance). Antibiotics with poor or no anaerobic activity: aminoglycosides, aztreonam, most cephalosporins (insufficient Bacteroides cover without metronidazole addition), fluoroquinolones (variable Bacteroides activity).
What is the role of metronidazole in anaerobic infection?
Metronidazole is the drug of choice for most anaerobic infections and has excellent activity against gram-negative anaerobes (Bacteroides, Prevotella, Fusobacterium) and Clostridium species. It is also the treatment of choice for CDI, Trichomonas, and Giardia. It works by being reduced to a toxic nitro-radical in anaerobic organisms (which have nitroreductase activity) that damages DNA. Aerobic organisms lack the reductive metabolic pathways to activate metronidazole, explaining its selectivity for anaerobes.