Routine use of microbial whole genome sequencing in diagnostic and public health microbiology
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.
Citation
Koeser , C U , Ellington , M J , Cartwright , E J P , Gillespie , S H , Brown , N M , Farrington , M , Holden , M T G , Dougan , G , Bentley , S D , Parkhill , J & Peacock , S J 2012 , ' Routine use of microbial whole genome sequencing in diagnostic and public health microbiology ' , PLoS Pathogens , vol. 8 , no. 8 , e1002824 . https://doi.org/10.1371/journal.ppat.1002824
Publication
PLoS Pathogens
Status
Peer reviewed
ISSN
1553-7374Type
Journal item
Rights
© 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.
Description
This work is partly supported by funding from the Medical Research Council, the European Developing Country Clinical Trials Partnership, the Global Alliance for TB Drug Development, and the European Union.Collections
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