{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["16(1)"],"submitter":["Mixao V"],"funding":["Wellcome Trust"],"pubmed_abstract":["Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the d"],"journal":["Nature communications"],"pagination":["3961"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12038046"],"repository":["biostudies-literature"],"pubmed_title":["Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens."],"pmcid":["PMC12038046"],"pubmed_authors":["Borges V","Coipan CE","Radomski N","Majgaard Uldall AS","Deneke C","Simon S","Holtsmark Nielsen S","de Ruvo A","Dourado Santos J","Bucciacchio A","Petrovska L","Mixao V","Lagesen K","Grimstrup Joensen K","Sobral D","Linde J","Di Pasquale A","Iwan E","Castelli P","Bomba A","Pietsch M","Brendebach H","Kiil K","Gomes JP","Tausch SH","Kaas RS","Pinto M"],"additional_accession":[]},"is_claimable":false,"name":"Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.","description":"Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the d","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Apr","modification":"2026-06-01T10:17:36.798Z","creation":"2025-07-10T03:09:11.15Z"},"accession":"S-EPMC12038046","cross_references":{"pubmed":["40295532"],"doi":["10.1038/s41467-025-59246-8"]}}