4.3.1 Incubation atmosphere

Clinically relevant bacteria may be classified based on their atmospheric requirement into:

• anaerobic bacteria
• aerobic bacteria.

Anaerobic bacteria vary widely in their tolerance to atmospheric oxygen. For example, Bacteroides and Clostridium species are obligate anaerobes, whereas Enterobacteriaceae and some streptococci are facultative anaerobes. Similarly, aerobic bacteria differ in their oxygen requirements, from obligate aerobes such as mycobacteria and Bacillus species, to microaerophiles, such as Campylobacter spp.

Animal health laboratories incubate most specimens in aerobic and/or microaerophilic atmospheres, enabling the growth of aerobes, facultative aerobes and some aerotolerant anaerobes. Incubation in these two atmospheres may require separate incubators, but it can also be done in one aerobic incubator by placing the microaerophilic cultures inside jars with a controlled atmosphere (Figure 7).

Figure 7 An anaerobic work and incubation station, and anaerobic and microaerophilic jars that can be placed in a normal aerobic incubator

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An image of an anaerobic work and incubation station. The second image is of anaerobic and microaerophilic jars that can be placed in a normal aerobic incubator.

Figure 7 An anaerobic work and incubation station, and anaerobic and microaerophilic jars that can be placed in a normal aerobic incubator

Culture for obligate anaerobes requires strict specimen collection and transport techniques to prevent the exposure of the bacteria to the damaging effect of atmospheric oxygen during transport. In many animal health diagnostic laboratories, anaerobic culture is carried out only upon specific request. The identification of obligate anaerobes requires expertise and tests not widely available at regional laboratories, so many anaerobic infections in farm animals are routinely diagnosed using culture-free methods or not diagnosed at all (see Section 5.4.4).