title: Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.
abstract: BACKGROUND
  Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility of whole-genome sequencing in defining nosocomial VREfm transmission.
  
  
  METHODS
  A retrospective study at a single hospital in the United Kingdom identified 342 patients with E. faecium bloodstream infection over 7 years. Of these, 293 patients had a stored isolate and formed the basis for the study. The first stored isolate from each case was sequenced (200 VREfm [197 vanA, 2 vanB, and 1 isolate containing both vanA and vanB], 93 vancomycin-susceptible E. faecium) and epidemiological data were collected. Genomes were also available for E. faecium associated with bloodstream infections in 15 patients in neighboring hospitals, and 456 patients across the United Kingdom and Ireland.
  
  
  RESULTS
  The majority of infections in the 293 patients were hospital-acquired (n = 249) or healthcare-associated (n = 42). Phylogenetic analysis showed that 291 of 293 isolates resided in a hospital-associated clade that contained numerous discrete clusters of closely related isolates, indicative of multiple introductions into the hospital followed by clonal expansion associated with transmission. Fine-scale analysis of 6 exemplar phylogenetic clusters containing isolates from 93 patients (32%) identified complex transmission routes that spanned numerous wards and years, extending beyond the detection of conventional infection control. These contained both vancomycin-resistant and -susceptible isolates. We also identified closely related isolates from patients at Cambridge University Hospitals NHS Foundation Trust and regional and national hospitals, suggesting interhospital transmission.
  
  
  CONCLUSIONS
  These findings provide important insights for infection control practice and signpost areas for interventions. We conclude that sequencing represents a powerful tool for the enhanced surveillance and control of nosocomial E. faecium transmission and infection.
authors.affiliation: Department of Medicine, University of Cambridge.
authors.forename: Kathy E
authors.initials: KE
authors.lastname: Raven
authors.affiliation: Department of Medicine, University of Cambridge.|Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and.|Cambridge University Hospitals NHS Foundation Trust, Cambridge.
authors.forename: Theodore
authors.initials: T
authors.lastname: Gouliouris
authors.affiliation: Department of Medicine, University of Cambridge.
authors.forename: Hayley
authors.initials: H
authors.lastname: Brodrick
authors.affiliation: London School of Hygiene and Tropical Medicine.
authors.forename: Francesc
authors.initials: F
authors.lastname: Coll
authors.affiliation: Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and.|Cambridge University Hospitals NHS Foundation Trust, Cambridge.
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Brown
authors.affiliation: British Society for Antimicrobial Chemotherapy, Birmingham.|North Bristol NHS Trust, Southmead Hospital, Bristol; and.
authors.forename: Rosy
authors.initials: R
authors.lastname: Reynolds
authors.affiliation: Department of Medicine, University of Cambridge.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: Department of Medicine, University of Cambridge.|Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, and.|Cambridge University Hospitals NHS Foundation Trust, Cambridge.
authors.forename: M Estée
authors.initials: ME
authors.lastname: Török
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Department of Medicine, University of Cambridge.|Cambridge University Hospitals NHS Foundation Trust, Cambridge.|London School of Hygiene and Tropical Medicine.|Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
mesh_terms: D003428:Cross Infection; D016984:Enterococcus faecium / Q000145:classification / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D016680:Genome, Bacterial; D016908:Gram-Positive Bacterial Infections / Q000382:microbiology* / Q000635:transmission*; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012189:Retrospective Studies; D065507:Vancomycin-Resistant Enterococci; D000073336:Whole Genome Sequencing
keywords: Enterococcus faecium; genome sequencing.; infection control; transmission; vancomycin resistant