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

Published: 27 December 2012



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.


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.


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.