First report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat

Abstract

We isolated a highly colistin-resistant Escherichia coli, strain 58, from fresh chicken wings in Lebanon. Here, we performed in-depth phenotypic and genomic analyses to identify the resistome of the isolate, focusing on the determinants that encoded colistin resistance. The minimum inhibitory concentration (MIC) of colistin and resistance to other antibiotics were determined using the broth microdilution method and the Kirby-Bauer disk diffusion assay, respectively. Whole-genome sequencing (WGS) and different software available at the Center of Genomic Epidemiology were used to predict the resistome, the sequence type (ST), and the presence of virulence genes and plasmid replicon types. Susceptibility testing revealed that E. coli 58 exhibited multidrug resistance, including against colistin (MIC=32 µg/mL). Whole-genome sequencing analyses showed that E. coli 58 carried 26 antimicrobial resistance genes associated with resistance to polymyxins (mcr-1.26), β-lactams (blaTEM-1b and blaCMY-2), fosfomycin (fosA4), aminoglycosides (aac(3)-IId, aadA2b, aadA5, partial aadA1, aph(3'')-Ia, aph(3')-Ia, and aph(6)-Id), tetracyclines (tetA and tetM), quinolones (qnrS1), sulphonamides (sul2 and sul3), trimethoprim (dfrA14, dfrA17, and dfrA5), phenicols (floR and cmlA1), macrolides (mphA), lincosamides (lnu(F)), quaternary ammonium compounds (partial qacL and qacE), and peroxides (sitABCD). mcr-1.26 was located on an IncX4 plasmid and induced colistin resistance in otherwise naïve E. coli and Salmonella Enteritidis. Escherichia coli 58 was predicted to be a human pathogen and belonged to ST3107. To our knowledge, this is the first report of mcr-1.26 in poultry meat worldwide. We previously reported mcr-1.26 in an MDR E. coli (ST2207) isolated from a pigeon in Lebanon, which suggests that it might be spreading in different animal hosts and genetic backgrounds.