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

Richard G. Everitt, Xavier Didelot, Elizabeth M. Batty, Ruth R. Miller, Kyle Knox, Bernadette C. Young, Rory Bowden, Adam Auton, Antonina Votintseva, Hanna Larner-Svensson, Jane Charlesworth, Tanya Golubchik, Camilla L.C. Ip, Heather Godwin, Rowena Fung, Tim E.A. Peto, A. Sarah Walker, Derrick W. Crook, Daniel J. Wilson

Research output: Contribution to journalArticlepeer-review

103 Scopus citations


Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island vSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype-phenotype mapping.

Original languageEnglish (US)
Article number3956
JournalNature communications
StatePublished - May 23 2014
Externally publishedYes

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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