One of the first steps in selecting an appropriate antibiotic is to know about the target bacteria. This can be accomplished through culture which is the growth of bacterial organisms in media. Samples from the site of infection of an individual animal or a collection of samples from a herd or flock can be used to determine the characteristics of the bacterial organism of concern.
Culture will also determine if the target bacterium is aerobic, microaerophilic, or anaerobic (facultative or obligate), which is also important when selecting an antibiotic. For example, uptake of aminoglycosides into a bacterium uses an oxygen-dependent mechanism. Aminoglycosides are less active against anaerobes, but can be particularly active against aerobic bacteria.
Center for Food Security and Public Health