D-BeONE.1.1 Report on the state of the art

JRP24-FBZSH9-BEONE WP1 deliverable 1.1.

WP Leader: Vítor Borges (INSA)

Other contributors: Verónica Mixão (INSA), Miguel Pinto (INSA), Karin Lagesen (NVI), Eve Zeyl Fiskebeck (NVI), Hakon Kaspersen (NVI), Camilla Sekse (NVI), Thomas H. A. Haverkamp (NVI) and other members of the ORION project.

As a joint collaboration with the ORION project within the One Health EJP, the BeONE project WP1-T1 has contributed to the compilation of an online HandBook covering the current state of the art of WGS-typing methods for One Health surveillance. Such a resource is expected to contribute to the success not only of the other BeONE WPs, but also, at a broader scale, to the scientific community and all the staff from public health institutions which are now transitioning between technologies.

The One Health Sequencing for Surveillance HandBook is available through the link https://oh-sfs-handbook.readthedocs.io/en/latest/ and is currently divided in the following sections:

• “Sequencing technologies”, covering technical aspects of the currently available sequencing platforms; 
• “Bioinformatics methods”, providing an overview of the different steps of a bioinformatics pipeline for WGS data analysis (from file formats and quality control to genome assembly); 
• “Single isolate typing methods and resources”, providing an overview of topics such as MLST, Serotyping, Virulence and AMR detection, among others; 
• “Clustering methods and resources”, covering topics such as cgMLST, SNP and allele calling, and phylogenetics; 
• “Compute infrastructure”, covering the computational aspects of WGS data analysis, from workflows managers to the available platforms for the analysis; 
• “Species specific toolchains”, providing a historical revision of the different typing methods used for L. monocytogenes, S. enterica, E. coli and C. jejuni until the advent of WGS. This section also covers the WGS data analysis specificities of each of these species, from their specific culture needs, DNA extraction protocols, bioinformatics pipelines (cgMLST and SNP-based pipelines), to their outbreak definition thresholds, medically relevant genes recognized thus far and the state of their One Health surveillance; 
• “Challenges for One Health Surveillance”, providing an overview of the relevance of implementing enhanced One Health surveillance frameworks, and exploring the challenges that are associated with the demanding WGS technological transition at inter-sectoral level.