Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology | Genetics and Genomics | JAMA Internal Medicine | JAMA Network
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Original Investigation
August 12/26, 2013

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

Author Affiliations
  • 1Wellcome Trust Sanger Institute, Hinxton, England
  • 2Clinical Microbiology and Public Health Laboratory, Cambridge, England
  • 3Department of Medicine, University of Cambridge, Cambridge, England
  • 4Cambridge University Hospitals NHS Foundation Trust, Cambridge, England
  • 5Illumina Ltd, Great Chesterford, England
JAMA Intern Med. 2013;173(15):1397-1404. doi:10.1001/jamainternmed.2013.7734

Importance  The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens.

Objective  To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens.

Design, Setting, and Participants  A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information.

Main Outcomes and Measures  Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data.

Results  We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these.

Conclusions and Relevance  The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.