D-BeONE.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.