title: Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium.
abstract: Reasons for the rising clinical impact of the bacterium Enterococcus faecium include the species' rapid acquisition of adaptive genetic elements. Here, we focused on the impact of recombination on the evolution of E. faecium. We used the recently developed BratNextGen algorithm to detect recombinant regions in the core genome of 34 E. faecium strains, including three newly sequenced clinical strains. Recombination was found to have a significant impact on the E. faecium genome: of the original 1.2 million positions in the core genome, 0.5 million were predicted to have been affected by recombination in at least one strain. Importantly, strains in one of the two major E. faecium clades (clade B), which contains most of the E. faecium human gut commensals, formed the most important reservoir for donating foreign DNA to the second major E. faecium clade (clade A), which contains most of the clinical isolates. Also, several genomic regions were found to mainly recombine in specific hospital-associated E. faecium strains. One of these regions (the epa-like locus) likely encodes the biosynthesis of cell wall polysaccharides. These findings suggest a crucial role for recombination in the emergence of E. faecium as a successful hospital-associated pathogen.
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands. m.debeen-2@umcutrecht.nl
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.forename: Lu
authors.initials: L
authors.lastname: Cheng
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.forename: Rob J
authors.initials: RJ
authors.lastname: Willems
mesh_terms: D000220:Adaptation, Biological; D000465:Algorithms; D000668:Ampicillin Resistance / Q000235:genetics; D004269:DNA, Bacterial; D004274:DNA, Recombinant; D016984:Enterococcus faecium / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011995:Recombination, Genetic
chemical_list: D004269:DNA, Bacterial; D004274:DNA, Recombinant
keywords: BratNextGen; antibiotic resistance; comparative genomics; nosocomial pathogen; phylogenomics; whole-genome sequencing