Author(s):
Mixão, Verónica ; Pinto, Miguel ; Brendebach, Holger ; Sobral, Daniel ; Santos, João Dourado ; Radomski, Nicolas ; Uldall, Anne Sophie Majgaard ; Bomba, Arkadiusz ; Pietsch, Michael ; Bucciacchio, Andrea ; de Ruvo, Andrea ; Castelli, Pierluigi ; Iwan, Ewelina ; Simon, Sandra ; Coipan, Claudia E. ; Linde, Jörg ; Petrovska, Liljana ; Kaas, Rolf Sommer ; Joensen, Katrine Grimstrup ; Nielsen, Sofie Holtsmark ; Kiil, Kristoffer ; Lagesen, Karin ; Di Pasquale, Adriano ; Gomes, João Paulo ; Deneke, Carlus ; Tausch, Simon H. ; Borges, Vítor
Date: 2025
Persistent ID: http://hdl.handle.net/10400.18/10624
Origin: Repositório Científico do Instituto Nacional de Saúde
Subject(s): Bacterial Infection; Listeria; Bacterial Genomics; Genome Informatics; Policy and Public Health in Microbiology; Disease Outbreaks; Foodborne Diseases; Políticas de Saúde; Infecções Gastrointestinais
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 different resolution power of allele-based schemas led to marked discrepancies. Still, we identified non-negligible differences in outbreak detection and demonstrated how a threshold flexibilization favors the detection of similar outbreak signals by different laboratories. These results, together with the observation that different traditional typing groups (e.g., serotypes) exhibit a remarkably different genetic diversity, represent valuable information for future outbreak case-definitions and WGS-based nomenclature design. This study reinforces the need, while demonstrating the feasibility, of conducting continuous pipeline comparability assessments, and opens good perspectives for a smoother international and intersectoral cooperation towards an efficient One Health FWD surveillance.
