Interplay between bacterial clones and plasmids in the spread of bla SHV-12- and bla CTX-M-14-carrying Escherichia coli 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 Escherichia coli (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 (n = 7) and broiler farms (n = 8) in La Rioja (Spain) for Whole-Genome Sequencing (WGS). ESBL-E. coli isolates from a broiler farm (BF) all carried the bla SHV-12 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 bla CTX-M-14 gene associated with ST453/ST542/ST4038, and 6/7 isolates co-harboured the colistin-resistance mcr-1.1 gene. The bla CTX-M-14 genes were located on IncI1 (90-110 kpb) or IncF plasmids (100-110 kpb), while the bla SHV-12 ones were located on IncHI2 (220-250 kbp) or on IncF plasmids (150-180 kpb). IncF-bla CTX-M-14 and IncHI2-bla SHV-12 plasmids carried additional genes mostly inserted in class 1 integrons (intI1-dfrA17-aadA5-qacE-sul1 or intI1-estX-psp-aadA2-cmlA1-aadA-qacL-IS440-sul3 respectively). The mcr-1.1 gene was located on an IncX4 plasmid (33 kpb). Pig and poultry production systems lead to the selection of different bla ESBL genes, and both contributed to the global burden of antimicrobial resistance.