Prevalence and Genomic Characterization of mcr-1-Positive Escherichia coli from Livestock in Hunan Province, China (2016–2021)

In response to the critical challenge of colistin resistance in animal production, we examined the occurrence and genetic features of mcr-1-positive E. coli isolates collected from livestock in Hunan province, China, between 2016 and 2021. A total of 1,358 animal samples from chickens and pigs were collected and screened. Monitoring data indicates that nineteen mcr-1-positive E. coli isolates (1.40%) were identified, and all were resistant to colistin and tetracycline. The prevalence rate of mcr-1 positive E. coli has significantly declined since 2017 and has remained consistently low. Most isolates (89.47%) exhibited multidrug resistance and carried multiple antibiotic resistance genes, including tet(A), sul3, bla_TEM-1B, while a subset of strains (21.05%) harbored quinolone resistance-associated point mutations in gyrA, parC, and parE. Multi-locus sequence typing identified 14 sequence types, with ST48 being the most frequent (21.05%), and five clonal complexes, with CC10 as the predominant lineage (52.63%). Plasmid analysis revealed that 68.42% of the isolates carried plasmids, predominantly IncX4 (36.84%), and 57.89% of isolates harbored conjugative plasmids with complete relaxase and MPF system components. The mcr-1 gene was found within three main genetic arrangements: (i) mcr-1-pap2, (ii)ISApl1-mcr-1-pap2, and (iii) ISApl1-mcr-1-pap2-ISApl1. These findings highlight the potential for dissemination of mcr-1 in animal-derived E. coli and underscore the importance of monitoring and controlling antimicrobial resistance in livestock.