The contribution of population genetics to the epidemiological tracing of pathogenic bacteria: the predominant clonal evolution model

This article aims to present the specific contribution of population genetics and evolutionary genetics to the molecular tracing of epidemiological routes in bacteria pathogenic to humans and animals. More specifically, the “predominant clonal evolution” (PCE) model is exposed in details. It suggests that bacterial lineages are stable in space and time, from the macroevolutionary scale down to the level of microevolution (a time and space scale of a few years and kilometers, i. e., “measurably evolving pathogens”). This stability is a “si ne qua non” to make epidemiological tracing reliable. The PCE model does not state that genetic recombination is absent in bacteria, but merely that its impact is insufficient to break the pattern of predominant clonal evolution (clonal frame, multilocus bifurcating trees, linkage disequilibrium, stable multilocus genotypes). A few illustrative examples are drawn from major species: Escherichia coli , Mycobacterium tuberculosis , Neisseria meningitidis and Staphylococcus aureus .