Anaerobic Bacteria

Anaerobes are organisms unable to grow in the presence of atmospheric oxygen, typically lacking the enzymes, superoxide dismutase, catalase, needed to detoxify reactive oxygen species generated during aerobic metabolism.

This section covers the medically important anaerobes other than the spore-forming clostridia, which are dominated by distinctive, potent, single-organism toxin-mediated disease. The organisms here instead cause disease predominantly through polymicrobial, endogenous infection.

Anaerobes constitute the overwhelming majority of the human gastrointestinal microbiota by cell count. In the colon they outnumber aerobic and facultative organisms such as E. coli by a factor of roughly 100 to 1000. They are also major components of the normal oral, upper respiratory tract, and vaginal flora.

Because of this abundance, essentially all clinically significant anaerobic infection is endogenous. It arises from the patient's own flora translocating into a normally sterile site, not from exogenous acquisition. This shapes both the epidemiology and the specimen-interpretation principles for the whole organism group.

Anaerobic infection characteristically arises in tissue with reduced oxygen tension:

• devitalised or necrotic tissue
• deep wounds with poor blood supply
• abscess cavities, which are themselves low-oxygen environments once established and create a self-perpetuating condition favouring continued anaerobic growth
• sites adjacent to mucosal surfaces with abundant anaerobic flora: bowel perforation, dental infection, aspiration into the lower respiratory tract

This tissue-condition dependency is why anaerobic infection is disproportionately associated with specific clinical scenarios:

• intra-abdominal infection following bowel perforation or surgery
• aspiration pneumonia and lung abscess
• deep dental and oropharyngeal infection
• diabetic foot infection
• deep, penetrating, or crush-type wounds

Cutibacterium acnes, formerly Propionibacterium acnes, is a Gram positive, non-spore-forming, anaerobic, aerotolerant rod. It is a normal component of skin flora, particularly abundant in sebaceous, hair-follicle-rich areas.

It has low intrinsic virulence, but is implicated in the pathogenesis of acne vulgaris via follicular colonisation and the associated inflammatory response. Given its skin origin, it is a recognised cause of prosthetic device infection, particularly prosthetic joints (especially shoulder arthroplasty) and cerebrospinal fluid shunts.

Its slow growth and low apparent virulence can mean it is initially dismissed as a contaminant before being recognised as a genuine, indolent pathogen. This is a specific diagnostic pitfall.

Actinomyces species are Gram positive, branching, filamentous anaerobic or microaerophilic rods. They are normal flora of the oral cavity, gastrointestinal tract, and female genital tract.

They cause actinomycosis, a chronic, slowly progressive, suppurative and fibrosing infection. It characteristically crosses normal tissue planes and fascial boundaries, which helps to distinguish it from malignancy on imaging, although the clinical presentation can otherwise closely mimic cancer.

It classically produces draining sinus tracts containing sulfur granules. These are yellow, macroscopic aggregates of the organism and do not actually contain sulfur despite the name.

Classic clinical associations:

• Cervicofacial disease, following dental infection or oral trauma or procedures.
• Thoracic disease, following aspiration.
• Abdominal or pelvic disease, associated in particular with long-term intrauterine device use, a specific and recognised organism-device link.

Bacteroides fragilis is the single most clinically important anaerobic Gram negative bacillus, and the most common anaerobic isolate from clinically significant intra-abdominal infection specifically. It is normal flora of the colon, the dominant single organism by cell count in the human gut overall. It possesses a polysaccharide capsule, an unusual virulence feature among anaerobes generally, contributing to abscess formation and providing some protection against phagocytosis.

Bacteroides fragilis is a major cause of intra-abdominal abscess and polymicrobial intra-abdominal infection. It typically occurs alongside facultative Gram negative organisms such as E. coli, reflecting the mixed colonic flora from which the infection arises, following bowel perforation, diverticulitis, appendiceal perforation, or intra-abdominal surgery.

It shows a comparatively higher rate of intrinsic and acquired beta-lactamase production than most other anaerobes. This matters when selecting empirical antibiotic coverage for suspected intra-abdominal anaerobic infection. Agents active against beta-lactamase-producing anaerobes are required, such as metronidazole, carbapenems, or beta-lactam and beta-lactamase inhibitor combinations.

Prevotella species are Gram negative anaerobic bacilli, normal flora of the oral cavity and, to a lesser extent, the female genital tract. They are associated particularly with oral and dental infection, periodontal disease, dental abscess, aspiration pneumonia and lung abscess following oropharyngeal aspiration, and, in the genital tract, with bacterial vaginosis and pelvic infection.

Fusobacterium species are Gram negative anaerobic bacilli, normal oropharyngeal flora. They are associated with oropharyngeal and dental infection, and specifically implicated in Lemierre's syndrome.

Lemierre's syndrome is a rare but important complication of oropharyngeal infection, typically pharyngitis or peritonsillar abscess. The organism invades the adjacent internal jugular vein, causing septic thrombophlebitis with secondary septic pulmonary emboli. It is severe and potentially fatal, and most often affects previously healthy adolescents and young adults.

Anaerobic infection has three recurring, interlinked clinical hallmarks worth recognising as a cluster.

Abscess formation reflects a marked tendency for anaerobic infection to localise into a walled-off cavity rather than spreading diffusely, reflecting both the tissue-necrosis-favouring conditions and the low-oxygen microenvironment the abscess itself creates and perpetuates. Abscess formation is also the direct clinical reason surgical drainage, not antibiotics alone, is often the definitive treatment for anaerobic infection.

Foul-smelling infection results because anaerobic metabolism characteristically produces malodorous volatile fatty acid byproducts, so a foul or putrid odour from a wound, abscess, or sputum sample is a classic bedside clue strongly suggesting anaerobic involvement, useful even before formal culture results are available.

Polymicrobial infection is the norm rather than the exception. This follows from the polymicrobial nature of normal flora at the sites from which anaerobic infection typically arises, oral cavity, colon.

Anaerobic infection is very frequently mixed, involving multiple anaerobic species together with facultative aerobic or anaerobic organisms, such as E. coli in intra-abdominal infection, or viridans streptococci in oral and dental infection. It does not usually present as a pure single-organism infection.

This is directly relevant to both culture interpretation and the selection of sufficiently broad empirical antibiotic coverage.

Because anaerobes are killed by oxygen exposure, specimen collection and transport require specific precautions not needed for aerobic organisms.

Specimens should be collected directly from the infected site, as aspirated pus or deep tissue. A superficial swab is more likely to be contaminated by aerotolerant surface flora and less likely to yield fastidious anaerobes reliably.

Transport specimens promptly in anaerobic transport media or an oxygen-excluding container. Prolonged air exposure before the specimen reaches the laboratory can cause loss of organism viability and a falsely negative culture.

A superficial swab of a wound or ulcer is generally an inadequate specimen for reliable anaerobic culture. Clinicians are expected to request aspirated fluid or deep tissue specifically where anaerobic infection is genuinely suspected.