title: Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.
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.
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramírez
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.forename: Pekka
authors.initials: P
authors.lastname: Marttinen
authors.forename: Mona
authors.initials: M
authors.lastname: Aldeljawi
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.forename: Henrik
authors.initials: H
authors.lastname: Westh
authors.forename: Kit
authors.initials: K
authors.lastname: Boye
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Gulay
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Holden
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
mesh_terms: D001499:Bayes Theorem; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D058974:Phylogeography; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014421:Turkey