Interplay between bacterial clones and plasmids in the spread of - and -carrying from the livestock environment.

To better understand the role of broiler and pig farms as reservoirs and disseminating vehicles of Extended-Spectrum β-lactamase (ESBL)-producing (Ec), we performed a phylogenomic and plasmid analysis with a holistic view (human-animal-environmental interface). Here, we selected 15 ESBL-Ec recovered from the slurry, manure or air of pig ( = 7) and broiler farms ( = 8) in La Rioja (Spain) for Whole-Genome Sequencing (WGS). ESBL- isolates from a broiler farm (BF) all carried the gene associated with ST68/ST117/ST770/ST1684 and the new genetic lineage ST15985. On the contrary, all those from a pig farm (PF) carried the gene associated with ST453/ST542/ST4038, and 6/7 isolates co-harboured the colistin-resistance gene. The genes were located on IncI1 (90-110 kpb) or IncF plasmids (100-110 kpb), while the ones were located on IncHI2 (220-250 kbp) or on IncF plasmids (150-180 kpb). IncF- and IncHI2- plasmids carried additional genes mostly inserted in class 1 integrons ( or -IS- respectively). The gene was located on an IncX4 plasmid (33 kpb). Pig and poultry production systems lead to the selection of different genes, and both contributed to the global burden of antimicrobial resistance.