Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens
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 effo...
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Nature Portfolio
2025-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59246-8 |
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| author | Verónica Mixão Miguel Pinto Holger Brendebach Daniel Sobral João Dourado Santos Nicolas Radomski Anne Sophie Majgaard Uldall Arkadiusz Bomba Michael Pietsch Andrea Bucciacchio Andrea de 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 Di Pasquale João Paulo Gomes Carlus Deneke Simon H. Tausch Vítor Borges |
| author_facet | Verónica Mixão Miguel Pinto Holger Brendebach Daniel Sobral João Dourado Santos Nicolas Radomski Anne Sophie Majgaard Uldall Arkadiusz Bomba Michael Pietsch Andrea Bucciacchio Andrea de 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 Di Pasquale João Paulo Gomes Carlus Deneke Simon H. Tausch Vítor Borges |
| author_sort | Verónica Mixão |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-6df58c832a81441ebcf1d65542e1309c |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-6df58c832a81441ebcf1d65542e1309c2025-08-20T02:10:50ZengNature PortfolioNature Communications2041-17232025-04-0116112710.1038/s41467-025-59246-8Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogensVerónica Mixão0Miguel Pinto1Holger Brendebach2Daniel Sobral3João Dourado Santos4Nicolas Radomski5Anne Sophie Majgaard Uldall6Arkadiusz Bomba7Michael Pietsch8Andrea Bucciacchio9Andrea de Ruvo10Pierluigi Castelli11Ewelina Iwan12Sandra Simon13Claudia E. Coipan14Jörg Linde15Liljana Petrovska16Rolf Sommer Kaas17Katrine Grimstrup Joensen18Sofie Holtsmark Nielsen19Kristoffer Kiil20Karin Lagesen21Adriano Di Pasquale22João Paulo Gomes23Carlus Deneke24Simon H. Tausch25Vítor Borges26Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR)Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI)Department of Omics Analyses, National Veterinary Research Institute (PIWet)Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI)National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)Department of Omics Analyses, National Veterinary Research Institute (PIWet)Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI)Department for Infectious Diseases, Epidemiology and Surveillance, National Institute for Public Health and the Environment (RIVM)Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute (FLI)Animal and Plant Health Agency (APHA), AddlestoneNational Food Institute, Technical University of Denmark (DTU)Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI)Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI)Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI)Section for Epidemiology, Norwegian Veterinary Institute (NVI)National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM)Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR)National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR)Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA)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.https://doi.org/10.1038/s41467-025-59246-8 |
| spellingShingle | Verónica Mixão Miguel Pinto Holger Brendebach Daniel Sobral João Dourado Santos Nicolas Radomski Anne Sophie Majgaard Uldall Arkadiusz Bomba Michael Pietsch Andrea Bucciacchio Andrea de 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 Di Pasquale João Paulo Gomes Carlus Deneke Simon H. Tausch Vítor Borges Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens Nature Communications |
| title | Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| title_full | Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| title_fullStr | Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| title_full_unstemmed | Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| title_short | Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| title_sort | multi country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens |
| url | https://doi.org/10.1038/s41467-025-59246-8 |
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