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

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  • Richard G. Everitt

    (University of Oxford, John Radcliffe Hospital
    Present addresses: Department of Mathematics and Statistics, University of Reading, Reading RG6 6AX, UK (R.G.V.))

  • Xavier Didelot

    (University of Oxford
    Present addresses: Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK (X.D.))

  • Elizabeth M. Batty

    (University of Oxford
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

  • Ruth R Miller

    (University of Oxford, John Radcliffe Hospital)

  • Kyle Knox

    (University of Oxford)

  • Bernadette C. Young

    (University of Oxford, John Radcliffe Hospital)

  • Rory Bowden

    (University of Oxford
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

  • Adam Auton

    (Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

  • Antonina Votintseva

    (University of Oxford, John Radcliffe Hospital
    University of Oxford)

  • Hanna Larner-Svensson

    (University of Oxford, John Radcliffe Hospital
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

  • Jane Charlesworth

    (University of Oxford, John Radcliffe Hospital)

  • Tanya Golubchik

    (University of Oxford, John Radcliffe Hospital
    University of Oxford)

  • Camilla L. C. Ip

    (University of Oxford
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

  • Heather Godwin

    (Oxford University Hospitals National Health Service Trust, John Radcliffe Hospital)

  • Rowena Fung

    (University of Oxford, John Radcliffe Hospital)

  • Tim E. A. Peto

    (University of Oxford, John Radcliffe Hospital)

  • A. Sarah Walker

    (University of Oxford, John Radcliffe Hospital)

  • Derrick W. Crook

    (University of Oxford, John Radcliffe Hospital)

  • Daniel J. Wilson

    (University of Oxford, John Radcliffe Hospital
    Wellcome Trust Centre for Human Genetics, Roosevelt Drive)

Abstract

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 νSaα. 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.

Suggested Citation

  • 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 , 2014. "Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus," Nature Communications, Nature, vol. 5(1), pages 1-9, September.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4956
    DOI: 10.1038/ncomms4956
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    Cited by:

    1. Francesc Coll & Beth Blane & Katherine L. Bellis & Marta Matuszewska & Toska Wonfor & Dorota Jamrozy & Michelle S. Toleman & Joan A. Geoghegan & Julian Parkhill & Ruth C. Massey & Sharon J. Peacock & , 2025. "The mutational landscape of Staphylococcus aureus during colonisation," Nature Communications, Nature, vol. 16(1), pages 1-15, December.

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