NGS data of Dutch STEC isolates for source attribution models.. Dutch input in DiSCoVer - One Health EJP WP2; discovering the sources of STEC

Dutch STEC isolates from various sources were shared within the DiSCoVer consortium. For human data it was decided to limit the analysis to 2010-2020, whereas isolates from non-human sources isolated earlier were also included. Pets, wildlife and environmental samples had a priority for inclusion and for any sampling performed within the project since previous collections prioritized on human isolates and domestic ruminants. To harmonize bioinformatics analyses the same pipeline via the ARIES galaxy platform was used. This Discover pipeline performs trimming and de novo assembly (SPAdes 3.12) followed by serotyping, MLST (7 genes) analysis, stx subtyping, virulotyping, AMR gene detection and cgMLST: allele calling. Generated profiles served as input for various source attribution models.