Title |
Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus
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Published in |
Genome Biology, December 2012
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DOI | 10.1186/gb-2012-13-12-r126 |
Pubmed ID | |
Authors |
Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil |
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. |
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United States | 3 | 17% |
Netherlands | 2 | 11% |
Germany | 2 | 11% |
Australia | 1 | 6% |
Unknown | 6 | 33% |
Demographic breakdown
Type | Count | As % |
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Scientists | 10 | 56% |
Members of the public | 6 | 33% |
Science communicators (journalists, bloggers, editors) | 2 | 11% |
Mendeley readers
Geographical breakdown
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Brazil | 2 | 1% |
Sweden | 2 | 1% |
Portugal | 1 | <1% |
United Kingdom | 1 | <1% |
Denmark | 1 | <1% |
United States | 1 | <1% |
Unknown | 131 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 35 | 25% |
Student > Ph. D. Student | 34 | 24% |
Student > Bachelor | 14 | 10% |
Student > Doctoral Student | 11 | 8% |
Professor > Associate Professor | 7 | 5% |
Other | 20 | 14% |
Unknown | 18 | 13% |
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Agricultural and Biological Sciences | 58 | 42% |
Biochemistry, Genetics and Molecular Biology | 14 | 10% |
Medicine and Dentistry | 11 | 8% |
Immunology and Microbiology | 9 | 6% |
Computer Science | 6 | 4% |
Other | 11 | 8% |
Unknown | 30 | 22% |