PATH-SAFE consortium recommendations for genomic surveillance of food-borne diseases Escherichia coli and Listeria monocytogenes

Gally, David, Maiden, Martin, Jolley, Keith, McIntyre, K. Marie, Ott, Sascha, Darby, Alistair, Loman, Nick, Kingsley, Robert A., Chalka, Antonia, Holt, Kathryn, McNally, Alan, Baker, Kate, Avison, Matthew, AbuOun, Manal, Graham, David, Jenkins, Claire, Chattaway, Marie, Nair, Satheesh, Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Vallejo-Trujillo, Adriana, King, Jason, Haynes, Edward, Ellis, Richard, McElhiney, Jacqui, Dorey-Robinson, Daniel, Gilmour, Matthew, Painset, Anaïs, Egli, Adrian, Reimer, Aleisha, Mather, Alison, Allard, Marc, Stevens, Eric, Yahara, Koji, Lehours, Phillippe, Seemann, Torsten, Jenkins, Claire, Hendriksen, Rene S., Aarestrup, Frank, Aanensen, David, Acton, Richard, Alikhan, Nabil-Fareed, 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 food-borne diseases Escherichia coli and Listeria monocytogenes. FSA Research and Evidence 10.46756/001c.143984

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Abstract

Whole-genome sequencing (WGS) for food-borne 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 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 (the PATH-SAFE platform) will offer a trusted environment for WGS data sharing and analysis for UK agencies involved in FBD surveillance. Following the successful implementation of the platform for Salmonella, in the second phase the platform will be expanded to Escherichia coli and Listeria monocytogenes. Where possible, the platform will draw on existing and validated solutions. For de novo genome assembly, EToKI and vanilla SPAdes provide the best results for E. coli, and Pathogenwatch provides the best results for L. monocytogenes. Analysis of genomic data is greatly enhanced by assigning genomes into well-defined cluster groups, which should be available on the PATH-SAFE platform. Specifically, tools for MLST and cgMLST should be available on the PATH-SAFE platform for both E. coli and L. monocytogenes. In addition, HierCC and ClermonTyping tools should be available for E. coli. The platform should implement tools for clustering E. coli and L. monocytogenes based on MLST/cgMLST profiles. Clusters should be named according to their HierCC codes. The PATH-SAFE platform should implement a tool for predicting E. coli serotypes from sequence data. ECTyper has been selected as the only up-to-date tool for this purpose. Although serotype determination of E. coli isolates is useful for historical reasons, the platform should be designed in a way that makes it easy to switch to hierarchical clustering of isolates. The identification of genetic virulence determinants is essential in the analysis of E. coli and L. monocytogenes. VirulenceFinder and AdhesiomeR should be implemented in the PATH-SAFE platform for virulence determinant identification in E. coli. The Pasteur L. monocytogenes Scheme has been selected for virulence determinant identification in L. monocytogenes, although none of the available databases seems to include all known genes determining virulence in L. monocytogenes. As the PATH-SAFE platform is expanded to new food-borne pathogens, integrating a tool to differentiate species will be useful. Speciator has been validated and shown to be 99.9% in agreement with Kraken in correctly assigning E. coli genomes. The number of metadata fields should be small initially to facilitate upload of data and use of the PATH-SAFE platform and to be consistent with UK GDPR obligations. Minimum metadata requirements of the platform should be compatible with the metadata collected by each agency. They should also be compatible with concerns around data sharing and legal obligations. All metadata must be processed in line with UK GDPR guidelines and align with organisational policies and relevant legislation. The PATH-SAFE platform should implement a gated access model that will allow participating agencies to share additional metadata with trusted partners and at the same time minimise the risk of leaking sensitive information. The PATH-SAFE platform should have an automated QC mechanism for validating uploaded metadata. Options for both bulk upload of metadata and for upload of individual metadata fields should be offered by the platform. In addition, functionality for regular automated uploads could be provided. Experiences with implementing WGS for FBD surveillance in the UK, Switzerland and Canada show that collaboration of reference laboratories carrying out sequencing analyses and epidemiological and One Health units providing metadata is critical for prioritising isolates for outbreak investigations.

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 10:01
URI:	https://orca.cardiff.ac.uk/id/eprint/181651

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