Abstract
International audience; Aim: The protozoa Cryptosporidium parvum and Giardia duodenalis are causes of diarrhoeal disease in humans and animals.Typing schemes available to differentiate between isolates often lack resolution, limiting infection source tracing and outbreak characterisation. To develop novel typing schemes, the PARADISE project is generating whole genome sequencing (WGS) data for identification of loci with high genetic variability.Methods: Isolates of C. parvum (n=55) and G. duodenalis assemblage B (n=25) were collected from across Europe, and processed to extract high-quality genomic DNA for WGS (Illumina). For identification of variable regions, two bioinformatics pipelines were established. Common criteria to select variable regions included the number of Single Nucleotide Polymorphisms(SNPs), their distribution on chromosomes, and their relative usefulness in distinguishing between isolates within a population.Results: High quality genome drafts were obtained for almost all isolates. Raw sequence data processing identified about 100 highly variable genomic regions within C. parvum and G. duodenalis assemblage B.Conclusions: The large dataset of WGS data has enabled better evaluation of the overall genetic variability in C. parvum and G. duodenalis at the European level. The loci identified with high genetic variability are being evaluated for inclusion in novel genotyping schemes. This should improve both source attribution and knowledge of the molecular epidemiology of these zoonotic pathogens.