Deliverable D-JRP15–FED-AMR-WP3.2: Overview of genetic overlap between human and non-human Clostridiodes difficile isolates

This deliverable and the associated task aims to contribute to increase knowledge regarding the true impact of C. difficile as a zoonotic agent and its transmission networks, by evaluating the extent of genetic overlap and potential transmission between human and non-human C. difficile lineages. Whole-genome sequencing data from strains isolated from different sources were analysed in order to: i) infer the phylogenetic relationship between strains, through the alignment of genomes and extraction of core single-nucleotide variant positions, ii) describe the general trends of the core-genome determined within the dataset, and iii) identification of mobile genetic elements. In line with this, within WP3-T3, several studies were conducted with that purpose, involving several sampling campaigns to obtain isolates from animals, food and environment, focusing on relevant zoonotic C. difficile lineages. ST11 is considered one of the most pathogenic C. difficile types and a common type identified in many international studies, both from clinical and veterinary environments.