biostudies-literatureUnknown16(1)Mixao VWellcome TrustDifferent 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 dNature communications3961https://www.ebi.ac.uk/biostudies/studies/S-EPMC12038046biostudies-literatureMulti-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.PMC12038046Borges VCoipan CERadomski NMajgaard Uldall ASDeneke CSimon SHoltsmark Nielsen Sde Ruvo ADourado Santos JBucciacchio APetrovska LMixao VLagesen KGrimstrup Joensen KSobral DLinde JDi Pasquale AIwan ECastelli PBomba APietsch MBrendebach HKiil KGomes JPTausch SHKaas RSPinto MfalseMulti-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.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 d2025-01-01T00:00:00Z2025 Apr2026-06-01T10:17:36.798Z2025-07-10T03:09:11.15ZS-EPMC120380464029553210.1038/s41467-025-59246-8