Molecular Characterization of Colistin-Resistant Escherichia coli Isolated from Chickens: First Report from Nepal.

Dissemination of mcr-1 encoding colistin resistance in Gram-negative bacteria has created critical situation in poultry, livestock farming, and public health. In Nepal, for the first time, we initiated surveillance of colistin-resistant Escherichia coli in broilers from seven different chicken farms. A total of 324 cloacal swabs were collected and 118 E. coli were isolated, of which 27 (22.8%) were colistin resistance all harboring mcr-1 gene, but lacking ISApI1. Colistin-resistant isolates were characterized by antibiotic susceptibility testing, detecting antibiotic resistance genes, phylogenetic analysis, and plasmid replicon typing. These isolates belonged to the phylo-group A (70.37%) and phylo-group D (29.63%). In addition, most isolates (>80%) were resistant to ciprofloxacin, tetracycline, and sulfamethoxazole-trimethoprim. As much as 3 of the 27 mcr-1 encoding isolates were confirmed as extended-spectrum β-lactamase (ESBL) producer, all 3 isolates carrying blaCTX-M gene. We performed the conjugation experiment to check transferability of mcr-1, tet, and blaCTX-M genes, and only two donors were found to have transferred resistance to ticarcillin. The transfer of colistin and tetracycline resistance was not detected, which suggests the chromosomal location of mcr-1 and tet genes. The prevalence of Inc K/B and Inc I1 was 96.3% and 81.48%, respectively. This study shows the co-existence of mcr-1 with tet, sul, qnr, dfr, and blaCTX-M genes and dissemination of these resistant isolates in Nepalese chicken farms, which may pose huge threat to the livestock, especially chickens, and public health in Nepal.