PATH-SAFE consortium recommendations for genomic surveillance of foodborne diseases, using Salmonella as an exemplar

Dallman, Tim, Maiden, Martin, Jolley, Keith, McIntyre, Marie, Gally, David, Ott, Sascha, Darby, Alistair, Loman, Nick, Hinton, Jay, Kingsley, Robert A, Holt, Kathryn, Wheeler, Nicole, Graham, David, Chattaway, Marie, Nair, Satheesh, Connor, Tom ORCID: https://orcid.org/0000-0003-2394-6504, Traka, Maria, Vallejo-Trujillo, Adriana, King, Jason, Haynes, Edward, Daspan, Tigan, Line, Kirsty, Ellis, Richard, Callaghan, Kathryn, James, Marianne, Larkin, Lesley, Petrovska, Liljana, Gilmour, Matthew, Mather, Alison, Allard, Marc, Stevens, Eric, Yahara, Koji, Lehours, Phillippe, Seemann, Torsten, Jenkins, Claire, Hendriksen, Rene S., Aarestrup, Frank, Aanensen, David, Acton, Richard, Blanton, Angela, Baker, James, Walker, Jude, Lewis-Woodhouse, Georgina, Connor, Diana, Yeats, Corin, Abudahab, Khalil, Shinde, Pranit and Vegvari, Carolin 2025. PATH-SAFE consortium recommendations for genomic surveillance of foodborne diseases, using Salmonella as an exemplar. FSA Research and Evidence 10.46756/001c.143833

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Abstract

Whole-genome sequencing (WGS) for foodborne disease (FBD) surveillance provides many benefits, including new insights in disease transmission, virulence and antimicrobial resistance (AMR), fast and precise outbreak tracing and source attribution, as well as, enabling streamlined and reproducible analysis through digital data that from a technical point of view can be easily shared. The National foodborne disease genomic data platform, developed as part of the PATH-SAFE programme, will offer a trusted environment for WGS data sharing and analysis for UK agencies involved in FBD surveillance. The platform has initially been built for Salmonella with the intention to expand it to other organisms later. Where possible, the platform has drawn on existing and validated solutions as implemented in EnteroBase, PubMLST and Pathogenwatch. The platform is hosted on CLIMB-BIG-DATA and has been built to enable interoperability between analytical tools and databases. Although a fully interoperable bioinformatics system for FBD and AMR surveillance is not practically feasible at this time, it should be a long-term goal. Recommendations on which tools to use for molecular surveillance of Salmonella have been developed in consultation with Community Input Advisory Groups (CIAGs) on 1) technical aspects of FBD surveillance, 2) AMR risk determinants, 3) data standards for FBD surveillance, 4) considerations for international molecular FBD surveillance. The purpose of this document is to act as a standard reference for methodologies for genomic surveillance of FBD to support FSA goals and achieve the benefits laid out above. The recommendations have been developed using non-typhoidal Salmonella as an example.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Schools > Biosciences
Publisher:	Food Standards Agency
Date of First Compliant Deposit:	14 October 2025
Last Modified:	14 Oct 2025 09:47
URI:	https://orca.cardiff.ac.uk/id/eprint/181647

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