title: Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.
abstract: OBJECTIVE
  Pseudomonas aeruginosa is a common nosocomial pathogen responsible for significant morbidity and mortality internationally. Patients may become colonised or infected with P. aeruginosa after exposure to contaminated sources within the hospital environment. The aim of this study was to determine whether whole-genome sequencing (WGS) can be used to determine the source in a cohort of burns patients at high risk of P. aeruginosa acquisition.
  
  
  METHODS
  An observational prospective cohort study.
  
  
  METHODS
  Burns care ward and critical care ward in the UK.
  
  
  METHODS
  Patients with >7% total burns by surface area were recruited into the study.
  
  
  METHODS
  All patients were screened for P. aeruginosa on admission and samples taken from their immediate environment, including water. Screening patients who subsequently developed a positive P. aeruginosa microbiology result were subject to enhanced environmental surveillance. All isolates of P. aeruginosa were genome sequenced. Sequence analysis looked at similarity and relatedness between isolates.
  
  
  RESULTS
  WGS for 141 P. aeruginosa isolates were obtained from patients, hospital water and the ward environment. Phylogenetic analysis revealed eight distinct clades, with a single clade representing the majority of environmental isolates in the burns unit. Isolates from three patients had identical genotypes compared with water isolates from the same room. There was clear clustering of water isolates by room and outlet, allowing the source of acquisitions to be unambiguously identified. Whole-genome shotgun sequencing of biofilm DNA extracted from a thermostatic mixer valve revealed this was the source of a P. aeruginosa subpopulation previously detected in water. In the remaining two cases there was no clear link to the hospital environment.
  
  
  CONCLUSIONS
  This study reveals that WGS can be used for source tracking of P. aeruginosa in a hospital setting, and that acquisitions can be traced to a specific source within a hospital ward.
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Joshua
authors.initials: J
authors.lastname: Quick
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: Cumley
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Wearn
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Marc
authors.initials: M
authors.lastname: Niebel
authors.affiliation: Division of Microbiology and Immunology, University of Warwick, Warwick, UK.
authors.forename: Chrystala
authors.initials: C
authors.lastname: Constantinidou
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Thomas
authors.affiliation: Division of Microbiology and Immunology, University of Warwick, Warwick, UK.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK.
authors.forename: Naiem S
authors.initials: NS
authors.lastname: Moiemen
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK Healing Foundation Centre for Burns Research, University Hospital Birmingham Foundation Trust, Birmingham, UK.
authors.forename: Amy
authors.initials: A
authors.lastname: Bamford
authors.affiliation: NIHR Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital, Birmingham, UK.
authors.forename: Beryl
authors.initials: B
authors.lastname: Oppenheim
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Nicholas J
authors.identifier: http://orcid.org/0000-0002-9843-8988
authors.initials: NJ
authors.lastname: Loman
mesh_terms: D000328:Adult; D003428:Cross Infection / Q000382:microbiology*; D005260:Female; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D006761:Hospitals; D006801:Humans; D008297:Male; D011446:Prospective Studies; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000235:genetics*
keywords: BIOTECHNOLOGY & BIOINFORMATICS; MICROBIOLOGY