The project consists of two major areas of research:

(1) The compilation and whole genome sequencing of a representative strain collection from commensal and pathogenic E.coli from different hosts, animal as well as human and from different geographic origins. Besides NGS on the Illumina platform we will collect all relevant metadata for the isolates, including information on antimicrobial drug usage in humans and animals at the most detailed level possible. All primary data together with the genome sequences will be consolidated and stored in a central data warehouse for the consortium.

(2) Comprehensive bioinformatics analyses of the genome sequences to identify genomic elements that are associated with specific hosts. For this, first the phylogenetic relatedness of the strains based on the core genome will be determined to see if there exist certain clusters that originate from specific hosts. Furthermore, differences in the distribution and frequency of recombination events within the genomes will be analysed for correlation with host specificity. Next, small sequence parts will be searched within the core and accessory genome for statistically significant enrichment in the genomes of strains from specific hosts and the function of the corresponding genes or regulatory elements. Finally a detailed characterization of the mobile genetic elements that carry ESBL, carbapenemase and colistin resistance genes will be performed to determine the role of their incompatibility groups, conjugation systems, and co-located resistance genes in how they spread.

The project is part of a transnational research collaboration under the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR). The collaboration involves scientists from the UK, Germany, Spain and the Netherlands working together on a solution to this research question. The funding measure pursues the aim of bringing together relevant research groups with complementary expertise and resources from the participating countries. Cooperative research approaches will achieve progress in preventing, monitoring and combating antibiotic resistance which could not be achieved on a national level.