Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens

Verónica Mixão, Miguel Pinto, Holger Brendebach, Daniel Sobral, João Dourado Santos, Nicolas Radomski, Anne Sophie Majgaard Uldall, Arkadiusz Bomba, Michael Pietsch, Andrea Bucciacchio, Andrea Ruvo, Pierluigi Castelli, Ewelina Iwan, Sandra Simon, Claudia E. Coipan, Jörg Linde, Liljana Petrovska, Rolf Sommer Kaas, Katrine Grimstrup Joensen, Sofie Holtsmark Nielsen, Kristoffer Kiil, Karin Lagesen, Adriano Pasquale, João Paulo Gomes, Carlus Deneke, Simon H. Tausch and Vítor Borges ()
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Verónica Mixão: National Institute of Health Doutor Ricardo Jorge (INSA)
Miguel Pinto: National Institute of Health Doutor Ricardo Jorge (INSA)
Holger Brendebach: German Federal Institute for Risk Assessment (BfR)
Daniel Sobral: National Institute of Health Doutor Ricardo Jorge (INSA)
João Dourado Santos: National Institute of Health Doutor Ricardo Jorge (INSA)
Nicolas Radomski: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)
Anne Sophie Majgaard Uldall: Statens Serum Institut (SSI)
Arkadiusz Bomba: National Veterinary Research Institute (PIWet)
Michael Pietsch: Robert Koch Institute (RKI)
Andrea Bucciacchio: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)
Andrea Ruvo: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)
Pierluigi Castelli: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)
Ewelina Iwan: National Veterinary Research Institute (PIWet)
Sandra Simon: Robert Koch Institute (RKI)
Claudia E. Coipan: National Institute for Public Health and the Environment (RIVM)
Jörg Linde: Friedrich-Loeffler-Institute (FLI)
Liljana Petrovska: Addlestone
Rolf Sommer Kaas: Technical University of Denmark (DTU)
Katrine Grimstrup Joensen: Statens Serum Institut (SSI)
Sofie Holtsmark Nielsen: Statens Serum Institut (SSI)
Kristoffer Kiil: Statens Serum Institut (SSI)
Karin Lagesen: Norwegian Veterinary Institute (NVI)
Adriano Pasquale: Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)
João Paulo Gomes: National Institute of Health Doutor Ricardo Jorge (INSA)
Carlus Deneke: German Federal Institute for Risk Assessment (BfR)
Simon H. Tausch: German Federal Institute for Risk Assessment (BfR)
Vítor Borges: National Institute of Health Doutor Ricardo Jorge (INSA)

Nature Communications, 2025, vol. 16, issue 1, 1-27

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-59246-8

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