1. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology
- Author
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Mark Farrington, Edward J. P. Cartwright, Stephen H. Gillespie, Julian Parkhill, Claudio U. Köser, Nicholas M. Brown, Sharon J. Peacock, Matthew T. G. Holden, Matthew J. Ellington, Stephen D. Bentley, and Gordon Dougan
- Subjects
DNA, Bacterial ,lcsh:Immunologic diseases. Allergy ,medicine.medical_specialty ,Opinion ,Clinical Pathology ,Epidemiology ,Immunology ,Antimicrobial susceptibility ,Context (language use) ,Genomics ,Biology ,Microbiology ,Turnaround time ,Infectious Disease Epidemiology ,03 medical and health sciences ,Diagnostic Medicine ,Virology ,Genetics ,medicine ,Pathology ,Humans ,Molecular Biology ,lcsh:QH301-705.5 ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Diagnostic microbiology ,Bacteria ,030306 microbiology ,Public health ,Bacterial Infections ,Sequence Analysis, DNA ,3. Good health ,Clinical microbiology ,Clinical Microbiology ,lcsh:Biology (General) ,Medicine ,Parasitology ,lcsh:RC581-607 ,Genome, Bacterial - Abstract
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.
- Published
- 2012