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Pathophysiology, clinical clues, and recovery of organisms in anaerobic infections

John G Bartlett, MD
Section Editor
Stephen B Calderwood, MD
Deputy Editor
Sheila Bond, MD


Anaerobic bacteria are the major constituents of normal human flora at virtually all anatomic sites and have been recovered from a wide array of different infections. Isolating the organisms from specimens requires the use of specialized methods in the microbiology laboratory, but it has often been problematic to determine when these bacteria represent true pathogens or merely commensals. This decision is facilitated by the anaerobe recovered and its established pathogenic potential and concentration as well as the appropriateness of the specimen source.

The pathophysiology of anaerobic infections, clinical clues to suspect anaerobes, and methods for recovering the organisms will be reviewed here. Clinical syndromes involving anaerobes (including treatment), the history of anaerobes, and their role in the normal flora are discussed separately. (See "Anaerobic bacterial infections" and "Anaerobic bacteria: History and role in normal human flora".)


Anaerobic infections nearly always arise from leakage of endogenous bacteria into contiguous or other sites. Important exceptions are some of the clostridial syndromes, including botulism, Clostridium perfringens food poisoning, enteritis necroticans, tetanus, some cases of gas gangrene, and Clostridium difficile–associated diarrhea. (See related topics.)

The usual pathophysiologic mechanism for anaerobic infection is a breach in the mucocutaneous barrier resulting in displacement of the normal flora. Host defense mechanisms are presumably important, but the compromised host is not unusually susceptible. Exceptions are infections associated with defects of mucocutaneous barriers, such as carcinoma with obstruction, mucositis, perirectal lesions, or compromised consciousness with aspiration.

Three major issues arise in the pathogenesis of anaerobic infections:

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Literature review current through: Nov 2017. | This topic last updated: Aug 23, 2017.
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