Abundance of mobilized colistin resistance gene mcr-1 in genetically diverse commensal Escherichia coli in broiler chicken in Bangladesh

Background: Resistance to colistin in Escherichia coli can be due to mutations in the chromosome or, as reported very recently, plasmid-mediated transferable genes called mobilized colistin resistance (mcr) genes. There are nine mcr genes (mcr-1 to mcr-9) identified so far. Their presence and distribution in bacterial pathogens in poultry in Bangladesh are unknown, although extensive use of colistin in poultry is seen in the country.

Methods and materials: A total of 1200 E. coli strains were isolated from fecal samples collected from 20 broiler farms at three-time points of production. They were investigated by a multiplex PCR to detect the presence of five mcr genes (mcr-1 to mcr-5). The diversity in strains isolated were assessed by repetitive extragenic palindromic (REP)-PCR fingerprinting followed by genomic characterization and phylogenetic comparison in the genomes of 32 strains randomly selected in the dominant REP-types among the mcr-1 positive isolates.

Results: The results revealed that 25% (95% CI, 23–28%) of the isolates obtained were positive for the mcr-1 gene. The minimum inhibitory concentration (MIC) values of colistin sulphate to the mcr-1 positive E. coli strains varied from 2 to 128 mg/L. As many as 367 unique profiles were seen in the isolates by REP-PCR with a high ecological diversity index (Shannon diversity index, H’, of 5.3). By genome analysis, 42 acquired antimicrobial resistance genes (ARGs) were detected in the 32 E. coli strains.

Conclusion: There is high abundance of commensal E.coli strains carrying the mcr-1 gene in poultry in Bangladesh and the strains are genetically diverse, suggesting a massive horizontal spread of the gene rather by clonal expansion.