D-BeONE.1.3 Clustering congruence and thresholds

Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Mixão, Verónica;
Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Pinto, Miguel;
Affiliation
National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
Brendebach, Holger;
Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Sobral, Daniel;
Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Santos, João Dourado;
Affiliation
National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
Radomski, Nicolas;
Affiliation
Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
Uldall, Anne Sophie Majgaard;
Affiliation
Department of Omic Analyses, National Veterinary Research Institute (PIWet), Puławy, Poland
Bomba, Arkadiusz;
Affiliation
Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI), Wernigerode, Germany
Pietsch, Michael;
Affiliation
National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
Bucciacchio, Andrea;
Affiliation
National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
Rinaldi, Antonio;
Affiliation
National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
Castelli, Pierluigi;
Affiliation
Department of Omic Analyses, National Veterinary Research Institute (PIWet), Puławy, Poland
Iwan, Ewelina;
Affiliation
Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI), Wernigerode, Germany
Simon, Sandra;
Affiliation
National Institute for Public Health and the Environment (RIVM), The Netherlands
Swart-Coipan, Claudia;
GND
1022638580
VIAF
258250032
Affiliation
Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute (FLI), Jena, Germany
Linde, Jörg;
Affiliation
Animal and Plant Health Agency (APHA), United Kingdom
Petrovska-Holmes, Liljana;
Affiliation
National Food Institute, Technical University of Denmark (DTU), Lyngby, Denmark
Kaas, Rolf Sommer;
Affiliation
Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
Joensen, Katrine Grimstrup;
Affiliation
Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
Nielsen, Sofie Holtsmark;
Affiliation
Norwegian Veterinary Institute (NVI), Norway
Lagesen, Karin;
Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Gomes, João Paulo;
Affiliation
National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
Di Pasquale, Adriano;
Affiliation
National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, GermanyNational Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
Deneke, Carlus;
Affiliation
National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
Tausch, Simon H.;
Affiliation
Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
Borges, Vítor

Foodborne pathogens pose an important and serious threat to human and animal health. Therefore, genomics-based surveillance systems able to track the circulation of these pathogens and monitor their clinical and epidemiological relevant features have been implemented at the reference laboratories of multiple countries and sectors. However, there is a lack of harmonization between them that challenges the integration and comparison of data at international and intersectoral levels, and, ultimately, the establishment of fully integrative and efficient One Health genomic surveillance frameworks. In the BeONE project, we aimed to perform a massive comparison between different bioinformatics pipelines used for genomic surveillance of foodborne bacterial pathogens, as a way to assess the congruence and comparability of their clustering results. Specifically, BeONE WP1-T3 had as main objectives the:

  • Evaluation of the behavior of different surveillance-oriented genomics pipelines in the definition of genetic clusters, through the identification of threshold ranges with high resolution for outbreak detection or stable threshold ranges for nomenclature design (useful for longitudinal surveillance); 
  • Determination of the congruence with traditional typing nomenclatures, such as Sequence Type (ST) or serovar;
  • Identification of congruent resolution levels between pipelines, as a way to facilitate international data sharing and cooperation;
  • Assessment of the similarities and discrepancies between pipelines in the identification of outbreak-related isolates

In this repository, we provide the Deliverable of BeONE WP1-T3 with a brief overview of its activities and the preliminary results obtained until the end of the BeONE project. We anticipate that this study will provide important information regarding the behavior of each pipeline and facilitate the direct comparability of their results.

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