Genomic insights into epidemic plasmids carrying bla CTX-M and mcr-1 genes in Escherichia coli from Lebanese broiler production

In a previous nationwide survey in the Lebanese broiler production, multidrug-resistant CTX-M-producing were found to carry the mobile colistin resistance gene . To investigate the mobile genetic supports responsible for the spread of these resistance genes among in healthy broilers in Lebanon. Thirty-three and - positive of various sequence types from 17 broilers farms were subjected to conjugation assays. Long-read sequencing (Oxford Nanopore Technologies) and hybrid assembly were performed to determine complete plasmid sequences and their phylogenetic diversity. Twenty-nine conjugative IncFII plasmids harboured the extended-spectrum β-lactamase genes ( = 25) or ( = 4). Highly related IncF2:A-:B-/ plasmids differing only through IS-mediated genetic rearrangements in antibiotic resistance gene clusters were found in genetically diverse strains isolated from distant farms. The mobile colistin resistance genes and were carried by IncX4 and IncI2 plasmids. Worryingly, in one isolate, the IS - transposable unit was found integrated in a -carrying IncX4 plasmid. Beside expanded cephalosporins and colistin resistances, all isolates were multidrug-resistant with different additional resistances against aminoglycosides, (fluoro)quinolones, fosfomycin, phenicols, sulphonamides, tetracycline and trimethoprim. Closely related CTX-M-3/55-borne IncF2:A-:B- plasmids harbouring variable MDR regions and carrying IncX4 plasmids are widely disseminated in the population of healthy broilers in Lebanon. Further surveillance programmes of antimicrobial resistance and interventions to reduce the abusive use of medically important antibiotics are necessary to limit the spread of resistances in food-producing animals in Lebanon.