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We studied a commensal colistin-resistant  Escherichia coli  isolated from a swine cecum sample collected at a slaughter, in Portugal. Antimicrobial susceptibility phenotype of  E. coli  LV23529 showed resistance to colistin at a minimum inhibitory concentration of 4 mg/L. Whole genome of  E. coli  LV23529 was sequenced using a MiSeq system and the assembled contigs were analyzed for the presence of antibiotic resistance and plasmid replicon types using bioinformatics tools. We report a novel  mcr-1  gene variant ( mcr-1.9 ), carried by an IncX4 plasmid, where one-point mutation at nucleotide T1238C leads to Val413Ala substitution. The  mcr-1.9  genetic context was characterized by an IS 26  element upstream of the  mcr-pap2  element and by the absence of IS Apl1 . Bioinformatic analysis also revealed genes conferring resistance to β-lactams, sulphamethoxazole, trimethoprim, chloramphenicol and colistin, corresponding to the phenotype noticed. Moreover, we highlight the presence of  mcr-1.9  plus  bla  CTX-M-8 , a  bla  ESBL  gene rarely detected in Europe in isolates of animal origin; these two genes were located on different plasmids with 33,303 and 89,458 bp, respectively. MCR-1.9-harboring plasmid showed high identity to other X4-type  mcr-1 -harboring plasmids characterized worldwide, which strongly suggests that the presence of PMCR-encoding genes in food-producing animals, such as MCR-1.9, represent a potential threat to humans, as it is located in mobile genetic elements that have the potential to spread horizontally.

IncX4 Plasmid Carrying the New mcr-1.9 Gene Variant in a CTX-M-8-Producing Escherichia coli Isolate Recovered From Swine