title: Fighting outbreaks with bacterial genomics: case review and workflow proposal.
abstract: BACKGROUND
  Disease outbreak investigation is a key aspect of public health. Whole-genome sequencing of bacterial pathogen based on new generation high-throughput sequencing technologies has facilitated outbreak investigations recently. Whilst the approach has become more affordable and accessible to research and clinical laboratories, a system for adequate and efficient analyses of genome data in the context of bacterial outbreak investigations is missing.
  
  
  METHODS
  We performed a literature review of timely genomic investigations performed during the course of bacterial outbreaks that are based on new generation sequencing technologies. Currently available bioinformatics tools for genomic analyses are also reviewed here.
  
  
  RESULTS
  Genomic investigations in early stages of bacterial outbreaks have shown to provide timely information on evolutionary origin, transmission route, pathogenic potential, and resistance information of the outbreak strains and allow development of strain-specific typing methods. A systematic genomic analytical workflow is proposed here for the first time to facilitate efficient extraction of epidemiologically useful information from genome data of bacterial pathogens in future bacterial outbreak investigations.
  
  
  CONCLUSIONS
  With the continuous reduction of genome sequencing cost and development of user-friendly analytical tools, it is expected that high-throughput genome sequencing will be applied routinely for timely genomic analysis in bacterial outbreaks in the near future.
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: M K
authors.initials: MK
authors.lastname: Cheung
authors.forename: H S
authors.initials: HS
authors.lastname: Kwan
mesh_terms: D004196:Disease Outbreaks / Q000517:prevention & control*; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D058889:Molecular Typing; D057188:Workflow