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.
- View At a Glance
Clinical microbiology is a discipline that focuses on rapidly characterizing pathogen samples to direct the management of individual infected patients (diagnostic microbiology) and to monitor the epidemiology of infectious disease (public health microbiology). Applications in epidemiology include detecting outbreaks, monitoring trends in infection and identifying the emergence of new threats. Ongoing developments in DNA-sequencing technologies are likely to affect the diagnosis and monitoring of all pathogens, including viruses, bacteria, fungi and parasites, but for this Review we focus on bacterial pathogens to demonstrate the likely changes that arise from the adoption of routine whole-genome sequencing.