Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of untransformable species is incompletely understood. Here we identify widespread homologous recombination in the Staphylococcus aureus core genome, revealing a patchwork of hotspots and coldspots. We find that core recombination hotspots are situated near faultlines in the genome associated with mobile elements. Our results show that core genome transfer is driven by proximity to elements including phages, transposons and pathogenicity islands that can facilitate homologous recombination via integration at conserved sites and excision of core material. Mobile element-driven core genome transfer represents an important opportunity for adaptation and casts new light on the evolution of clonal pathogens. The consequences of core recombination on population structure are far-reaching, and improve the prospects for genome-wide association studies in these bacteria.