Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidatio n of evolutionary dynamics or phylogenetic relationships, population geneti cs of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart fi om being an essential component of these fundamental sciences, microbial typing clearly affects s everal areas of applied microbiogical research. The epidemiological investi gation of outbreaks of infectious diseases and the measurement of genetic d iversity in relation to relevant biological properties such as pathogenicit y, drug resistance, and biodegradation capacities al e obvious examples. Th e diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines te nd to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation The aim of the present review is to s ummarize the technological and fundamental concepts used in microbial taxon omy, evolutionary genetics, and epidemiology. Information on the nomenclatu re used in the different fields of research is provided, descriptions of th e diverse genetic typing procedures are presented, and examples of both con ceptual and technological research developments for Escherichia coli al e i ncluded Recommendations for unification of the different fields through sta ndardization of laboratory techniques are made.