Salmonella genomes deposited by VISAVET-UCM (Madrid, Spain) within the One Health European Joint Programme (OHEJP) DISCoVeR-ADONIS project

This project is part of the One Health European Joint Project. DISCoVeR (Discovering the sources of Salmonella, Campylobacter, VTEC and antimicrobial resistance). The objective of DISCoVeR are: to fill knowledge gaps regarding potential sources of foodborne zoonoses by including data on non-livestock reservoirs, non-food sources, pets and environmental sources (and their transmission routes) by providing source attribution estimates at different points in the exposure chain level and across EU regions and countries; to critically assess and improve existing source attribution models; and to use both phenotypic and genomic typing techniques for pathogen and antimicrobial resistance characterization, as well as epidemiological data, for the purposes of source attribution. ADONIS (Assessing Determinants of the Non-decreasing Incidence of Salmonella). The objective of ADONIS is to identify determinants underlying the stagnation/reversal of the decreasing trend in Salmonella Enteritidis incidence in humans and poultry in the EU. In the project the possible explanatory factors at the levels of primary production, epidemiology/exposure, and the pathogen itself are investigated under a cross-sectorial approach. All samples have been sequenced with Illumina and for nine isolates Nanopore reads (MinION) are also available. These last samples were originally sequenced in Sciensano (Belgium) and ITACYL (Spain). They have been analyzed in a broader WGS-based study, along with the Illumina reads of this project (and PRJEB73549), deposited by VISAVET-UCM