title: Whole genome sequencing in the prevention and control of Staphylococcus aureus infection.
abstract: BACKGROUND
  Staphylococcus aureus remains a leading cause of hospital-acquired infection but weaknesses inherent in currently available typing methods impede effective infection prevention and control. The high resolution offered by whole genome sequencing has the potential to revolutionise our understanding and management of S. aureus infection.
  
  
  OBJECTIVE
  To outline the practicalities of whole genome sequencing and discuss how it might shape future infection control practice.
  
  
  METHODS
  We review conventional typing methods and compare these with the potential offered by whole genome sequencing.
  
  
  RESULTS
  In contrast with conventional methods, whole genome sequencing discriminates down to single nucleotide differences and allows accurate characterisation of transmission events and outbreaks and additionally provides information about the genetic basis of phenotypic characteristics, including antibiotic susceptibility and virulence. However, translating its potential into routine practice will depend on affordability, acceptable turnaround times and on creating a reliable standardised bioinformatic infrastructure.
  
  
  CONCLUSIONS
  Whole genome sequencing has the potential to provide a universal test that facilitates outbreak investigation, enables the detection of emerging strains and predicts their clinical importance.
authors.affiliation: Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, UK. jrprice@doctors.org.uk
authors.forename: J R
authors.initials: JR
authors.lastname: Price
authors.forename: X
authors.initials: X
authors.lastname: Didelot
authors.forename: D W
authors.initials: DW
authors.lastname: Crook
authors.forename: M J
authors.initials: MJ
authors.lastname: Llewelyn
authors.forename: J
authors.initials: J
authors.lastname: Paul
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D003428:Cross Infection / Q000517:prevention & control*; D016680:Genome, Bacterial; D006801:Humans; D017053:Infection Control / Q000379:methods*; D017720:Molecular Epidemiology / Q000379:methods; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000382:microbiology / Q000517:prevention & control*; D013211:Staphylococcus aureus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification