The diversification of bacterial pathogens during infection is central to their capacity to adapt to different anatomical niches, evade the host immune system, and overcome therapeutic challenges. For example, antimicrobial treatment may fail due to the development of resistance during infection, which is often accompanied by transition to a less virulent state during chronic, persistent infection. In this review, the adaptation of the major human pathogen Staphylococcus aureus to its host environment during infection will be discussed, particularly in the context of new sequencing technologies which have opened a gateway towards understanding of the molecular processes underlying those adaptations. We now have the capacity to address previously intractable questions regarding bacterial diversification during infection which will ultimately lead to enhanced understanding of pathogenesis and the nature of epidemics, and will inform the design of effective therapeutic measures.
Keywords: Colonization; Evolution; Human; Infection; Staphylococcus aureus.
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