ABSTRACT
Epidemiological methods in microbiology include laboratory and analytical tools that are used to study the microbial distributions and determinants of infectious disease in host populations. The scope of this chapter is limited to a discussion of the tools that are used to study the molecular epidemiology of bacterial infectious disease. Natural populations of named bacterial species can accumulate immense levels of biological variation, but only a portion of their variation will contribute to their ability to cause infectious disease. Increasingly powerful tools have been developed to probe bacterial genomes for the variation of greatest epidemiological relevance. We discuss the criteria that are used to evaluate different tools, the concepts that are used to interpret the variation that is revealed by these tools, and the epidemiological applications for which these tools are deployed.
