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 and genomic epidemiology of bacterial infectious disease, but these tools have broader application for studying diseases caused by fungi, parasites, and viruses. Natural populations of named bacterial species can accumulate immense levels of genetic variation, and the now widespread use of whole genome sequencing has enabled this variation to be detected at the base-pair level across nearly complete genomes. Analysis of this genetic variation provides the basis for making epidemiological and evolutionary inferences about short-term bacterial transmission, longer-term bacterial evolution, and dispersal, and for identifying the precise bacterial determinants of disease. In this chapter, we discuss 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.
