Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut

This manuscript presents the phylogeny and conservation of IncK2 plasmids in Europe. It also provides insights into genetic traits responsible for IncK2 plasmids and its Escherichia coli host adaptation to the chicken gut. Fifty-eight E. coli isolates from nine European countries were sequenced using Illumina and Nanopore technology. Genetic analyses were performed to determine the relatedness of IncK2 plasmids and their E. coli hosts from poultry (80% of the total) and other sources. To analyse genetic traits associated with E. coli and IncK2 plasmid from chicken origin, a genome-wide association study (GWAS) was performed. The phylogenetic analysis of IncK2 plasmids revealed conservation across sources and countries of isolation. GWAS revealed multiple genes associated with IncK2 plasmids or its E. coli host from chicken origin. The predicted functions of these genes can indicate a selective advantage in the chicken gut, and that IncK2 plasmids are adapted to the physiological environment of the chicken gut.