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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Public Health | doi: 10.3389/fpubh.2019.00317

The Transformation of Reference Microbiology Methods and Surveillance for Salmonella with the use of Whole Genome Sequencing in England and Wales.

 Marie Anne Chattaway1*,  Tim Dallman1, Lesley Larkin1,  Satheesh Nair1, Jacquelyn McCormick1,  Amy Mikhail1,  Hassan Hartman1,  Gauri Godbole1, David Powell1, Martin Day1, Robert Smith1 and  Kathie Grant1
  • 1Public Health England, United Kingdom

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 (Taylor et al., 2015; Wuyts et al., 2015; Thomas et al., 2017). 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.

Keywords: WGS (Whole Genome Sequencing), Molecular Epidemiology, Genomic typing, Salmonella, SNP typing

Received: 27 Mar 2019; Accepted: 15 Oct 2019.

Copyright: © 2019 Chattaway, Dallman, Larkin, Nair, McCormick, Mikhail, Hartman, Godbole, Powell, Day, Smith and Grant. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Marie Anne Chattaway, Public Health England, London, United Kingdom, Marie.Chattaway@phe.gov.uk