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

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

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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
Pages (from-to)317
JournalFrontiers in public health
Volume7
DOIs
Publication statusPublished - 21 Nov 2019

Keywords / Materials (for Non-textual outputs)

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

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