PLoS Pathogens: Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
1 Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom, 2 Clinical Microbiology and Public Health Laboratory, Health Protection Agency Microbiology Services, Addenbrooke's Hospital, Cambridge, United Kingdom, 3 The Medical School University of St. Andrews, North Haugh, St. Andrews Fife, United Kingdom, 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 5 Department of Pathology, University of Cambridge, Cambridge, United Kingdom
Citation: Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, et al. (2012) Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology. PLoS Pathogens 8(8): e1002824. doi:10.1371/journal.ppat.1002824
Editor: Glenn F. Rall, The Fox Chase Cancer Center, United States of America
Published: August 2, 2012
Copyright: © 2012 Köser et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Parts of this work are based on CUK's Ph.D. research funded by a Gates Cambridge Scholarship, the Cambridge Philosophical Society, the Cambridge European Trust and Clare Hall, Cambridge. SJP receives grant funding from the Health Protection Agency, and from the UKCRC Translational Infection Research (TIR) Initiative supported by the Medical Research Council (Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, the Chief Scientist Office of the Scottish Government Health Directorates, and the Wellcome Trust. SJP and EJPC receive support from the NIHR Cambridge Biomedical Research Centre. MTGH, GD, SDB, and JP are supported by the Wellcome Trust. SHG receives grant funding from the Medical Research Council, the European Developing Country Clinical Trials Partnership, the Global Alliance for TB Drug Development, and the European Union. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: I have read the journal's policy and have the following conflicts: CUK, MJE, EJPC, NMB, MTGH, GD, SDB, JP, and SJP have collaborated with Illumina Ltd. on a number of scientific projects. JP has received funding for travel and accommodation from Pacific Biosciences Inc. and Illumina Inc. NMB is a consultant for Astellas Pharma Ltd. SHG has received payments from Bayer Schering Health Care for lectures. SJP is a consultant for Pfizer Inc. This does not alter our adherence to all PLoS Pathogens policies on sharing data and materials.
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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.