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Open Access Research

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

Santiago Castillo-Ramírez1, Jukka Corander2, Pekka Marttinen34, Mona Aldeljawi1, William P Hanage5, Henrik Westh67, Kit Boye6, Zeynep Gulay8, Stephen D Bentley9, Julian Parkhill9, Matthew T Holden9 and Edward J Feil1*

Author affiliations

1 Department of Biology and Biochemistry, University of Bath, Claverton Down Bath, Bath and North East Somerset BA2 7AY, UK

2 Department of Mathematics and Statistics, PO Box 68 (Gustaf Hällströmin katu 2b), University of Helsinki, FI-00014 Helsinki, Finland

3 Department of Information and Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, PO Box 15400 (Konemiehentie 2), FI-00076 Aalto, Finland

4 Department of Biomedical Engineering and Computational Science, Aalto University, PO Box 12200 (Rakentajanaukio 2c), FI-00076 Aalto, Finland

5 Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA

6 Department of Clinical Microbiology 445, Hvidovre Hospital, DK-2650 Hvidovre, Denmark

7 Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark

8 Dokuz Eylul University School of Medicine, Department of Clinical Microbiology, Mithatpaşa cad., Inciralti, Izmir 35340, Turkey

9 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

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Citation and License

Genome Biology 2012, 13:R126  doi:10.1186/gb-2012-13-12-r126

Published: 27 December 2012

Abstract

Background

Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bayesian approach, BRATNextGen, for detecting recombination on an expanded NGS dataset of the globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clone ST239.

Results

The data confirm strong geographical clustering at continental, national and city scales and demonstrate that the rate of recombination varies significantly between phylogeographic sub-groups representing independent introductions from Europe. These differences are most striking when mobile non-core genes are included, but remain apparent even when only considering the stable core genome. The monophyletic ST239 sub-group corresponding to isolates from South America shows heightened recombination, the sub-group predominantly from Asia shows an intermediate level, and a very low level of recombination is noted in a third sub-group representing a large collection from Turkey.

Conclusions

We show that the rapid global dissemination of a single pathogenic bacterial clone results in local variation in measured recombination rates. Possible explanatory variables include the size and time since emergence of each defined sub-population (as determined by the sampling frame), variation in transmission dynamics due to host movement, and changes in the bacterial genome affecting the propensity for recombination.