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

doi:10.1371/journal.ppat.1002824

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 journal › Editorial › peer-review

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.

Original language	English
Article number	e1002824
Number of pages	9
Journal	PLoS Pathogens
Volume	8
Issue number	8
DOIs	https://doi.org/10.1371/journal.ppat.1002824
Publication status	Published - 2 Aug 2012

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SDG 3 Good Health and Well-being

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10.1371/journal.ppat.1002824

Gillespie2012ppat1002824
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title = "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.",

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

note = "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.",

year = "2012",

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doi = "10.1371/journal.ppat.1002824",

language = "English",

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TY - JOUR

T1 - Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

AU - Koeser, Claudio U.

AU - Ellington, Matthew J.

AU - Cartwright, Edward J. P.

AU - Gillespie, Stephen H.

AU - Brown, Nicholas M.

AU - Farrington, Mark

AU - Holden, Matthew T. G.

AU - Dougan, Gordon

AU - Bentley, Stephen D.

AU - Parkhill, Julian

AU - Peacock, Sharon J.

N1 - 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.

PY - 2012/8/2

Y1 - 2012/8/2

N2 - 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.

AB - 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.

U2 - 10.1371/journal.ppat.1002824

DO - 10.1371/journal.ppat.1002824

M3 - Editorial

SN - 1553-7374

VL - 8

JO - PLoS Pathogens

JF - PLoS Pathogens

IS - 8

M1 - e1002824

ER -

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

Abstract

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