Population genetics

The rapid development of sequencing technology over recent years has both transformed molecular epidemiological surveillance and provided unprecedented detail concerning the molecular evolutionary processes occurring over very short time scales in bacterial pathogens. Here we review recent developments, with an emphasis on the application of next-generation sequencing platforms to understand the spread and diversification of methicillin-resistant Staphylococcus aureus (MRSA). We discuss how these datasets may provide information on transmission dynamics at different epidemiological scales, but also consider methods to gauge the strength of purifying selection acting on populations and subpopulations, and how this is likely to intersect with the ecology or epidemiology of different species or clones. We also discuss how these datasets are shedding light on other evolutionary properties of bacteria, such as genomic base composition, recombination, and mutation rate.