Advances_in_translation_of_genomics_to_diagnostics_and_public_health_microbiology-sc-2012-10-30T09:10:18Z-2421
Advances in translation of genomics to diagnostics and public health microbiology
Advances in translation of genomics to diagnostics and public health microbiology This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
"Rapid bacterial whole-genome sequencing to enhance diagnostic and   public health microbiology." Pubmed ID: 23857503. Rapid bacterial   whole-genome sequencing to enhance diagnostic and public health   microbiology. 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. 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.   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. 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. 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.