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Anaerobes comprise the predominant class of bacteria of the normal human microbiota (formerly termed “the normal human flora”) that reside on mucous membranes and predominate in many infectious processes, particularly those arising from mucosal surfaces. These organisms generally cause disease subsequent to the breakdown of mucosal barriers and the leakage of the microbiota into normally sterile sites. Infections resulting from contamination by the microbiota are usually polymicrobial and involve both aerobic and anaerobic bacteria. However, the difficulties encountered in handling specimens in which anaerobes may be important and the technical challenges entailed in cultivating and identifying these organisms in clinical microbiology laboratories continue to leave the anaerobic etiology of an infectious process unproven in many cases. Therefore, an understanding of the types of infections in which anaerobes can play a role is crucial in selecting appropriate microbiologic tools to identify the organisms in clinical specimens and in choosing the most appropriate treatment, including antibiotics and surgical drainage or debridement of the infected site.

This chapter focuses on infections caused by nonsporulating anaerobic bacteria. It does not address clostridial infections and syndromes, which are covered elsewhere (Chaps. 31 and 51).


Anaerobic bacteria are organisms that require reduced oxygen tension for growth, failing to grow on the surface of solid media in 10% CO2 in air. (In contrast, microaerophilic bacteria can grow in an atmosphere of 10% CO2 in air or under anaerobic or aerobic conditions, although they grow best in the presence of only a small amount of atmospheric oxygen, and facultative bacteria can grow in the presence or absence of air). Most clinically relevant anaerobes, such as Bacteroides fragilis, Prevotella melaninogenica, and Fusobacterium nucleatum, are relatively aerotolerant. Although they can survive for sustained periods in the presence of up to 2–8% oxygen, they generally do not multiply in this environment. A smaller number of pathogenic anaerobic bacteria (which are also part of the microbiota) die after brief contact with oxygen, even in low concentrations.


Most human mucocutaneous surfaces harbor a rich indigenous normal microbiota composed of aerobic and anaerobic bacteria. These surfaces are dominated by anaerobic bacteria, which often account for 99.0–99.9% of the culturable microbiota and range in concentration from 109/mL in saliva to 1012/mL in gingival scrapings and the colon. It is interesting that anaerobes inhabit many areas of the body that are exposed to air: skin, nose, mouth, and throat. Anaerobes are thought to reside in the portions of these sites that are relatively well protected from oxygen, such as gingival crevices. New technologies based on analyses of microbial DNA have expanded our knowledge of these bacterial populations. For example, in an analysis of 13,555 prokaryotic ribosomal RNA gene sequences from the colon, most bacteria identified were considered uncultivated and novel microorganisms. Two ...

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