Interplay between bacterial clones and plasmids in the spread of blaSHV-12- and blaCTX-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 <i>Escherichia coli</i> (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 (<i>n</i> = 7) and broiler farms (<i>n</i> = 8) in La Rioja (Spain) for Whole-Genome Sequencing (WGS). ESBL-<i>E. coli</i> isolates from a broiler farm (BF) all carried the <i>bla</i> _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 <i>bla</i> _CTX-M-14 gene associated with ST453/ST542/ST4038, and 6/7 isolates co-harboured the colistin-resistance <i>mcr-1.1</i> gene. The <i>bla</i> _CTX-M-14 genes were located on IncI1 (90-110 kpb) or IncF plasmids (100-110 kpb), while the <i>bla</i> _SHV-12 ones were located on IncHI2 (220-250 kbp) or on IncF plasmids (150-180 kpb). IncF-<i>bla</i> _CTX-M-14 and IncHI2-<i>bla</i> _SHV-12 plasmids carried additional genes mostly inserted in class 1 integrons (<i>intI1-dfrA17-aadA5-qacE-sul1</i> or <i>intI1-estX-psp-aadA2-cmlA1-aadA-qacL</i>-IS<i>440</i>-<i>sul3</i> respectively). The <i>mcr-1.1</i> gene was located on an IncX4 plasmid (33 kpb). Pig and poultry production systems lead to the selection of different <i>bla</i> _ESBL genes, and both contributed to the global burden of antimicrobial resistance.