D-BeONE.1.3 Clustering congruence and thresholds
Creators
- Verónica Mixão1
- Miguel Pinto1
- Holger Brendebach2
- Daniel Sobral1
- João Dourado Santos1
- Nicolas Radomski3
- Anne Sophie Majgaard Uldall4
- Arkadiusz Bomba5
- Michael Pietsch6
- Andrea Bucciacchio3
- Antonio Rinaldi3
- Pierluigi Castelli3
- Ewelina Iwan5
- Sandra Simon6
- Claudia Swart-Coipan7
- Jorg Linde8
- Liljana Petrovska-Holmes9
- Rolf Sommer Kaas10
- Katrine Grimstrup Joensen4
- Sofie Holtsmark Nielsen4
- Karin Lagesen11
- João Paulo Gomes1
- Adriano Di Pasquale3
- Carlus Deneke12
- Simon H. Tausch2
- Vítor Borges1
- 1. Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- 2. National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- 3. National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Italy
- 4. Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
- 5. Department of Omic Analyses, National Veterinary Research Institute (PIWet), Puławy, Poland
- 6. Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI), Wernigerode, Germany
- 7. National Institute for Public Health and the Environment (RIVM), The Netherlands
- 8. Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute (FLI), Jena, Germany
- 9. Animal and Plant Health Agency (APHA), United Kingdom
- 10. National Food Institute, Technical University of Denmark (DTU), Lyngby, Denmark
- 11. Norwegian Veterinary Institute (NVI), Norway
- 12. 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
Description
JRP24-FBZSH9-BEONE WP1 deliverable 1.3 (Clustering congruence and thresholds)
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.
Files
D-BeONE.1.3.pdf
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