title: Genomics and outbreak investigation: from sequence to consequence.
abstract: Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a significant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice.
authors.affiliation: Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK.
authors.forename: Esther R
authors.initials: ER
authors.lastname: Robinson
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, OX3 7LJ, UK.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Walker
authors.affiliation: Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen