A bacterium is considered anaerobic if it grows on solid media in the absence of O2 and fails to grow on solid media in air with increased concentration (10 %) CO2.

Anaerobic organisms are the predominant commensal organisms of the mouth, vagina, and GI tract and outnumber their aerobic “cousins” by at least a factor of 10 in making up “normal flora” of humans. There are more bacterial cells in and on humans than there are human cells and the majority are anaerobes.

Most disease associated with anaerobes is a result of physical and/or immunological derangement of areas contiguous with the mucosal surfaces where these organisms abound. That is, most disease is caused by endogenous organisms and usually several anaerobic and several aerobic organisms will be involved in the infective process (polymicrobial infection).

Important exceptions include tetanus and botulism, two classic toxin mediated diseases caused by species of Clostridia that are found in soil.

Common Clinical Isolates

Bacteroides fragilis (and group)

These small Gram negative rods are the most numerous commensals of the GI tract and most common anaerobic clinical isolates from patients with GI and gynecologic infection. They are of particular importance because of their ability to cause abscess formation and their relatively high rates of resistance to Beta-lactam antibiotics. Apart from this group, antibiotic resistance is relatively uncommon amongst anaerobes.

Fusobacterium spp.

These pleomorphic, long Gram negative rods often with tapered “pointy” ends are common in the mouth and GI tract. Their typical appearance in Gram stain is often a first clue that anaerobic organisms are involved in infective processes.

Porphyromonas spp. and Prevotella spp. (formerly pigmented “oral” Bacteroides)

Small Gram negative bacilli commonly involved in infections associated with the mouth and upper respiratory tract.

Peptostreptococcus spp.

Anaerobic streptococci. Commonly isolated from skin infections especially around the anus, perineum and inner thighs. Most often they are one of several organisms isolated.

Clostridium perfringens

Large, Gram positive, “boxcar” shaped rods that are the cause of clostridial myonecrosis or “gas gangrene” an emergent, rapidly progressive soft tissue infection that occurs after contaminated wounds or rarely after surgery. C. perfringens is readily identified in the laboratory by its characteristic “double zone” hemolysis.

C. perfringens also produces an enterotoxin and is an important cause of food borne illness especially associated with improperly stored cooked beef.

Clinical clues to the presence of anaerobes

  • Proximity to mucosal surfaces
  • Foul odour to pus
  • Disruption of GI tract or vagina/uterus
  • Gas in tissue
  • Bite wounds (human or animal)
  • Necrosis / Gangrene
  • Septic thrombophlebitis (esp. pelvic)

Laboratory clues to the presence of anaerobes

  • Specific morphotypes on Gram stain – pleomorphic, fusoform etc.
  • No growth on routine aerobic culture despite organisms on Gram stain smear
  • Growth deep in liquid media

Specific Clinical Diseases


Clostridium tetani is a ubiquitous soil organism that causes tetanus, by means of production of an exogenous neurotoxin while growing in infected wounds. Tetanus remains a common disease in the eloping world but has largely been controlled in North America by means of universal immunization with tetanus toxoid – inactivated tetanus toxin.

Toxin (tetanospasmin) binds irreversibly to presynaptic inhibitory neurons blocking release of inhibitory neurotransmitter resulting in unopposed excitatory activity and muscle spasm.

Lockjaw and opisthotonus are classic clinical manifestations of tetanus. Neonatal tetanus accounts for more than half of all deaths due to tetanus and its incidence may be very positively influenced by immunization programs aimed at mothers.

Further Reading

CDC Tetanus


An extremely serious cause of food associated disease; C. botulinum is also a ubiquitous soil organism that produces disease by elaborating a potent neurotoxin. Fortunately, attention to food processing and preservation make outbreaks very rare.

Improperly home canned foods and, in the far north the cultural practice of eating fermented seal and whale meat called muktuk are associated with most cases in Canada. There have been some large outbreaks associated with commercial foods including a celebrated case of contaminated “triple O” sauce at Whitespot restaurants in Vancouver in 1985.

Disease is manifest by flaccid paralysis induced by irreversible binding of toxin to pre-synaptic excitatory neurons. Neurological changes are symmetrical and sensory changes do not occur apart from vision difficulties secondary to extra-ocular muscle weakness that often occurs early in the course of illness.

Recovery is a very slow process taking many months, as neurons must be regenerated.

Further Reading

CDC Botulism

Clostridial myonecrosis (Gas Gangrene)

A feared complication of surgical or traumatic wounds, gas gangrene is one of the few infections that is a true medical emergency. C. perfringens is found worldwide in soil and is capable of producing many exotoxins. Other species of Clostridia are sometimes involved.

Disease is manifest by rapidly progressive skin changes with gas in tissue and extreme systemic “toxicity”. Emergent surgical debridement is imperative often resulting in amputation.

Diagnosis requires keen clinical suspicion and demonstration of gas in tissue by either palpation (crepitus) or X-ray. Confirmation by Gram stain of secretions or tissue showing typical “boxcar” shaped large Gram positive bacilli and very little cellular response should prompt aggressive therapy. In culture, C. perfringens produces characteristic “double zone” hemolysis on blood agar that makes presumptive identification easy.

Antibiotic associated diarrhea caused by Clostridium difficile

C. difficile is the cause a spectrum of diarrheal illness, from mild self limiting diarrhea through pseudomembranous colitis to toxic megacolon and death. It elaborates toxins while overgrowing other colonic flora after surviving antibiotic therapy. All antibiotics are capable of causing this problem with broad-spectrum cephalosporins and clindamycin being most associated.

Diagnosis centers on the demonstration of toxin in stool samples from patients who have had recent antibiotic therapy. The finding of the organism is of little diagnostic help as it may only reflect colonization, which is fairly common.

Spread of C. difficile among hospital patients is a problem and with the intense antibiotic use of modern medical care, outbreaks frequently occur. For this reason, particular care must be taken with the excrement of hospitalized patients with C. difficile disease.

This is a common illness and one of the reasons that prudent prescription of antibiotics is essential.

See Clostridium difficile management

Category: Microorganisms

Other Notes

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