The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Marie Anne Chattaway*, Tim Dallman, Lesley Larkin, Satheesh Nair, Jacquelyn McCormick, Amy Mikhail, Hassan Hartman, Gauri Godbole, David Powell, Martin Day, Robert Smith, Kathleen Grant

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

56 Citations (Scopus)

Abstract

The use of whole genome sequencing (WGS) as a method for supporting outbreak investigations, studying Salmonella microbial populations and improving understanding of pathogenicity has been well-described (1–3). However, performing WGS on a discrete dataset does not pose the same challenges as implementing WGS as a routine, reference microbiology service for public health surveillance. Challenges include translating WGS data into a useable format for laboratory reporting, clinical case management, Salmonella surveillance, and outbreak investigation as well as meeting the requirement to communicate that information in an understandable and universal language for clinical and public health action. Public Health England have been routinely sequencing all referred presumptive Salmonella isolates since 2014 which has transformed our approach to reference microbiology and surveillance. Here we describe an overview of the integrated methods for cross-disciplinary working, describe the challenges and provide a perspective on how WGS has impacted the laboratory and surveillance processes in England and Wales.

Original languageEnglish
Article number317
JournalFrontiers in Public Health
Volume7
DOIs
Publication statusPublished - 21 Nov 2019

Bibliographical note

Funding Information:
This study was funded by Public Health England and the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) (NIHR HPRU-2012-10038). The views expressed

Funding Information:
All of the diagnostic laboratories and the food, water and environmental laboratories of isolating and referring isolates to PHE. Thank you to Clare Maguire, Andrew Levy, and Anais Painset from GBRU for their support with the reference service. We would also like to thanks Cath Arnold and her team at the Whole Genome Sequencing Delivery Unit and Jonathan Green and his team at the Bioinformatics Unit at PHE for their support. Funding. This study was funded by Public Health England and the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) (NIHR HPRU-2012-10038). The views expressed are those of the author (s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England.

Keywords

  • SNP typing
  • Salmonella
  • WGS
  • genomic typing
  • molecular epidemiology

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