Nature Reviews Genetics 13, 601-612 (September 2012) | doi:10.1038/nrg3226

Article series: Applications of next-generation sequencing

Transforming clinical microbiology with bacterial genome sequencing

Xavier Didelot1, Rory Bowden1,2,3, Daniel J. Wilson2,4, Tim E. A. Peto3,4 & Derrick W. Crook4,3  About the authors


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 using 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. We predict that 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.

Author 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.

Correspondence to: Derrick W. Crook4,3 Email:

Published online 7 August 2012