phylogeographic variation in recombination rates within a global clone of methicillin-resistant staphylococcus aureus (mrsa)phylogeographic重组率的变化在全球克隆耐甲氧西林金黄色葡萄球菌(mrsa).pdf

Castillo-Ramírez et al. Genome Biology 2012, 13:R126 /2012/13/12/R126 RESEARCH Open Access Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus 1 2 3,4 1 5 Santiago Castillo-Ramírez , Jukka Corander , Pekka Marttinen , Mona Aldeljawi , William P Hanage , 6,7 6 8 9 9 9 Henrik Westh , Kit Boye , Zeynep Gulay , Stephen D Bentley , Julian Parkhill , Matthew T Holden and Edward J Feil1* 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 i