title: Whole Genome Sequencing in Real-Time Investigation and Management of a Pseudomonas aeruginosa Outbreak on a Neonatal Intensive Care Unit.
abstract: OBJECTIVE
  To use whole genome sequencing to describe the likely origin of an outbreak of Pseudomonas aeruginosa in a neonatal unit.
  
  
  METHODS
  Outbreak investigation.
  
  
  METHODS
  The neonatal intensive care unit service of a major obstetric tertiary referral center.
  
  
  METHODS
  Infants admitted to the neonatal unit who developed P. aeruginosa colonization or infection.
  
  
  METHODS
  We undertook whole genome sequencing of P. aeruginosa strains isolated from colonized infants and from the neonatal unit environment.
  
  
  RESULTS
  Eighteen infants were colonized with P. aeruginosa. Isolates from 12 infants and 7 environmental samples were sequenced. All but one of the clinical isolates clustered in ST253 and no differences were detected between unmapped reads. The environmental isolates revealed a variety of sequence types, indicating a large diverse bioburden within the unit, which was subsequently confirmed via enterobacterial repetitive intergenic consensus-polymerase chain reaction typing of post-outbreak isolates. One environmental isolate, obtained from a sink in the unit, clustered within ST253 and differed from the outbreak strain by 9 single-nucleotide polymorphisms only. This information allowed us to focus infection control activities on this sink.
  
  
  CONCLUSIONS
  Whole genome sequencing can provide detailed information in a clinically relevant time frame to aid management of outbreaks in critical patient management areas. The superior discriminatory power of this method makes it a powerful tool in infection control.
authors.affiliation: 1Department of Infectious Diseases and Microbiology,Royal Prince Alfred Hospital,Sydney NSW Australia.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Davis
authors.affiliation: 2Molecular Medicine Research Group,School of Medicine,University of Western Sydney,Sydney NSW Australia.
authors.forename: Slade O
authors.initials: SO
authors.lastname: Jensen
authors.affiliation: 1Department of Infectious Diseases and Microbiology,Royal Prince Alfred Hospital,Sydney NSW Australia.
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: Van Hal
authors.affiliation: 2Molecular Medicine Research Group,School of Medicine,University of Western Sydney,Sydney NSW Australia.
authors.forename: Björn
authors.initials: B
authors.lastname: Espedido
authors.affiliation: 4Department of Perinatal Medicine,Royal Prince Alfred Hospital,Sydney NSW Australia.
authors.forename: Adrienne
authors.initials: A
authors.lastname: Gordon
authors.affiliation: 1Department of Infectious Diseases and Microbiology,Royal Prince Alfred Hospital,Sydney NSW Australia.
authors.forename: Rima
authors.initials: R
authors.lastname: Farhat
authors.affiliation: 1Department of Infectious Diseases and Microbiology,Royal Prince Alfred Hospital,Sydney NSW Australia.
authors.forename: Raymond
authors.initials: R
authors.lastname: Chan
mesh_terms: D002353:Carrier State / Q000453:epidemiology / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D004196:Disease Outbreaks / Q000517:prevention & control*; D050456:Fomites / Q000382:microbiology; D016680:Genome, Bacterial; D006801:Humans; D015994:Incidence; D007223:Infant; D007231:Infant, Newborn; D007363:Intensive Care Units, Neonatal; D058885:Multilocus Sequence Typing; D020641:Polymorphism, Single Nucleotide; D011552:Pseudomonas Infections / Q000453:epidemiology* / Q000382:microbiology / Q000517:prevention & control; D011550:Pseudomonas aeruginosa / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial