title: Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.
abstract: OBJECTIVE
  Staphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation.
  
  
  METHODS
  Whole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny.
  
  
  RESULTS
  SNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A-G), of which four (A-D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication.
  
  
  CONCLUSIONS
  The presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.
authors.affiliation: Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway pauline.cavanagh@uit.no.
authors.forename: Jorunn Pauline
authors.initials: JP
authors.lastname: Cavanagh
authors.affiliation: Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Erik
authors.initials: E
authors.lastname: Hjerde
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.affiliation: Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Tim
authors.initials: T
authors.lastname: Kahlke
authors.affiliation: Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Claus
authors.initials: C
authors.lastname: Klingenberg
authors.affiliation: Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Trond
authors.initials: T
authors.lastname: Flægstad
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0SP, UK.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.
authors.forename: Johanna U Ericson
authors.initials: JU
authors.lastname: Sollid
mesh_terms: D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D005060:Europe / Q000453:epidemiology; D055106:Genome-Wide Association Study / Q000379:methods*; D006761:Hospitals / Q000639:trends*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D041162:Staphylococcus haemolyticus / Q000235:genetics* / Q000302:isolation & purification
keywords: SCCmec; bacterial genomics; molecular epidemiology; multidrug resistance; staphylococci