Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

Claudio U. Koeser, Matthew J. Ellington, Edward J. P. Cartwright, Stephen H. Gillespie, Nicholas M. Brown, Mark Farrington, Matthew T. G. Holden, Gordon Dougan, Stephen D. Bentley, Julian Parkhill, Sharon J. Peacock

Research output: Contribution to journalEditorialpeer-review

397 Citations (Scopus)


Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented.
Original languageEnglish
Article numbere1002824
Number of pages9
JournalPLoS Pathogens
Issue number8
Publication statusPublished - 2 Aug 2012


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