title: Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.
abstract: The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Méric
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal.
authors.forename: Maria
authors.initials: M
authors.lastname: Miragaia
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: de Been
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom The Biostatistics Center, Kurume University, Fukuoka, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Ben
authors.initials: B
authors.lastname: Pascoe
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Leonardos
authors.initials: L
authors.lastname: Mageiros
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Jane
authors.initials: J
authors.lastname: Mikhail
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Llinos G
authors.initials: LG
authors.lastname: Harris
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Wilkinson
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal.
authors.forename: Joana
authors.initials: J
authors.lastname: Rolo
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Lamble
authors.affiliation: Department of Zoology, University of Oxford, United Kingdom.
authors.forename: James E
authors.initials: JE
authors.lastname: Bray
authors.affiliation: Department of Zoology, University of Oxford, United Kingdom.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.affiliation: Center for Communicable Disease Dynamics, Harvard School of Public Health.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
authors.forename: Rory
authors.initials: R
authors.lastname: Bowden
authors.affiliation: Department of Zoology, University of Oxford, United Kingdom.
authors.forename: Martin C J
authors.initials: MC
authors.lastname: Maiden
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Dietrich
authors.initials: D
authors.lastname: Mack
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Hermínia
authors.initials: H
authors.lastname: de Lencastre
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.affiliation: College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom s.k.sheppard@swansea.ac.uk.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
mesh_terms: D055669:Ecological and Environmental Phenomena; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005800:Genes, Fungal; D014644:Genetic Variation; D016681:Genome, Fungal; D059765:Homologous Recombination; D013211:Staphylococcus aureus / Q000235:genetics*; D013212:Staphylococcus epidermidis / Q000235:genetics*
keywords: Staphylococcus; ecology; evolution; nosocomial infections; recombination