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<p>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: <i>Listeria monocytogenes</i>, <i>Salmonella enterica</i>, <i>Escherichia coli</i>, and <i>Campylobacter jejuni</i>. We found a general concordance between allele-based pipelines for all species, except for <i>C. jejuni</i>, 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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月28日

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  • 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

摘要

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.