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

2025-04-28Journal article Open access
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dc.contributor.authorMixão, Verónica
dc.contributor.authorPinto, Miguel
dc.contributor.authorBrendebach, Holger
dc.contributor.authorSobral, Daniel
dc.contributor.authorSantos, João Dourado
dc.contributor.authorRadomski, Nicolas
dc.contributor.authorUldall, Anne Sophie Majgaard
dc.contributor.authorBomba, Arkadiusz
dc.contributor.authorPietsch, Michael
dc.contributor.authorBucciacchio, Andrea
dc.contributor.authorde Ruvo, Andrea
dc.contributor.authorCastelli, Pierluigi
dc.contributor.authorIwan, Ewelina
dc.contributor.authorSimon, Sandra
dc.contributor.authorCoipan, Claudia E.
dc.contributor.authorLinde, Jörg
dc.contributor.authorPetrovska, Liljana
dc.contributor.authorKaas, Rolf Sommer
dc.contributor.authorJoensen, Katrine Grimstrup
dc.contributor.authorNielsen, Sofie Holtsmark
dc.contributor.authorKiil, Kristoffer
dc.contributor.authorLagesen, Karin
dc.contributor.authorDi Pasquale, Adriano
dc.contributor.authorGomes, João Paulo
dc.contributor.authorDeneke, Carlus
dc.contributor.authorTausch, Simon H.
dc.contributor.authorBorges, Vítor
dc.date.accessioned2025-11-20T11:31:14Z
dc.date.available2025-11-20T11:31:14Z
dc.date.issued2025-04-28
dc.description.abstractDifferent 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.eng
dc.description.sponsorshipINCD was funded by FCT and FEDER under the project 22153-01/SAICT/2016. We also thank the Italian Ministry of Health for supporting the acquisition of high-performance computing resources. This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust. This work was supported by co-funding from the European Union’s Horizon 2020 Research and Innovation program under grant agreement No 773830: One Health European Joint Programme (https://onehealthejp.eu/projects/foodborne-zoonoses/jrp-beone) (VB) and by the ISIDORe project (funding from the European Union’s Horizon Europe Research & Innovation Programme, Grant Agreement no. 101046133) (VB). VM contribution was funded by national funds through FCT - Foundation for Science and Technology, I.P., in the frame of Individual CEEC 2022.00851.CEECIND/CP1748/CT0001. JDS contribution was supported by the project “Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal'' (GENEO, https://www.insa.min-saude.pt/category/projectos/geneo/) on behalf of the EU4H programme (EU4H-2022-DGA-MS-IBA-1) (JPG). Research at the National Veterinary Research Institute (PIWet) Poland was supported by the Polish Ministry of Education and Science from the funds for science in the years 2018-2022 allocated for the implementation of a co-financed international project (EI).
dc.identifier.citationNat Commun. 2025 Apr 28;16(1):3961. doi: 10.1038/s41467-025-59246-8
dc.identifier.doi10.1038/s41467-025-59246-8
dc.identifier.eissn2041-1723
dc.identifier.pmid40295532
dc.identifier.urihttp://hdl.handle.net/10400.18/10624
dc.language.isoeng
dc.peerreviewedyes
dc.publisherNature Research
dc.relationPromoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.
dc.relationPathoGenSurveil - building dynamic workflows towards a sustainable and efficient genomics-informed pathogen surveillance
dc.relation.hasversionhttps://www.nature.com/articles/s41467-025-59246-8
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectBacterial Infection
dc.subjectListeria
dc.subjectBacterial Genomics
dc.subjectGenome Informatics
dc.subjectPolicy and Public Health in Microbiology
dc.subjectDisease Outbreaks
dc.subjectFoodborne Diseases
dc.subjectPolíticas de Saúde
dc.subjectInfecções Gastrointestinais
dc.titleMulti-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogenseng
dc.typejournal article
dcterms.referenceshttps://www.nature.com/articles/s41467-025-59246-8#Sec44
dspace.entity.typePublication
oaire.awardTitlePromoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.
oaire.awardTitlePathoGenSurveil - building dynamic workflows towards a sustainable and efficient genomics-informed pathogen surveillance
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/773830/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND5ed/2022.00851.CEECIND%2FCP1748%2FCT0001/PT
oaire.citation.issue1
oaire.citation.startPage3961
oaire.citation.titleNature Communications
oaire.citation.volume16
oaire.fundingStreamH2020
oaire.fundingStreamCEEC IND5ed
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
relation.isProjectOfPublication94d118fb-33ce-49fa-b1ed-d5bddf63581d
relation.isProjectOfPublicationcd3d705e-d6dd-4bf1-8b0e-0e3e0abc0b43
relation.isProjectOfPublication.latestForDiscovery94d118fb-33ce-49fa-b1ed-d5bddf63581d

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