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      Transforming clinical microbiology with bacterial genome sequencing

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          Abstract

          Whole genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here we review the current status of clinical microbiology and how it has already begun to be transformed by the use of next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. The application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

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          Author and article information

          Journal
          100962779
          22269
          Nat Rev Genet
          Nat. Rev. Genet.
          Nature reviews. Genetics
          1471-0056
          1471-0064
          1 October 2016
          07 August 2012
          September 2012
          04 October 2016
          : 13
          : 9
          : 601-612
          Affiliations
          [1 ]Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
          [2 ]Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
          [3 ]NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
          [4 ]Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
          Author notes
          Corresponding author DWC: derrick.crook@ 123456ndcls.ox.ac.uk
          Article
          PMC5049685 PMC5049685 5049685 ems70029
          10.1038/nrg3226
          5049685
          22868263
          ea48180d-a509-49cb-87c6-656a38d8ac6b
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