ABSTRACT
This chapter aims to a discussion of the tools that are used to study the molecular and genomic epidemiology of bacterial infectious disease, but these tools have broader application for studying diseases caused by fungi, parasites, and viruses. 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 chapter discusses the criteria that are used to evaluate different bacterial strain typing tools, the concepts that are used to interpret the genetic variation that is revealed by these tools, and the epidemiological applications for which these tools are deployed. Interpretive criteria have been proposed, but these criteria are specific for particular strain typing tools and particular epidemiological applications. In contrast, the experimental approach to virulence factor discovery that is often used in microbiology is based on assigning bacterial exposures in a laboratory microcosm.
