Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens
Mixão, Verónica Pinto, Miguel Brendebach, Holger Sobral, Daniel Dourado Santos, João Radomski, Nicolas Majgaard Uldall, Anne Sophie Bomba, Arkadiusz Pietsch, Michael Bucciacchio, Andrea
Mixão, Verónica
Pinto, Miguel
Brendebach, Holger
Sobral, Daniel
Dourado Santos, João
Radomski, Nicolas
Majgaard Uldall, Anne Sophie
Bomba, Arkadiusz
Pietsch, Michael
Bucciacchio, Andrea
Series / Report no.
Open Access
Type
Journal Article
Article
Article
Language
en
Date of publication
2025-04-28
Year of publication
Research Projects
Organizational Units
Journal Issue
Title
Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens
Translated Title
Published in
Nat Commun 2925; 16(1):3961
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 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.