Investigation and Molecular Characterization of Colistin Resistance in Commensal Escherichia coli Strains Isolated from Broiler Flocks

The emergence and dissemination of plasmid-mediated colistin resistance pose a serious threat to global public health. In this study, a total of 454 commensal Escherichia coli strains isolated from cloacal swabs taken from broiler flocks between 2013 and 2014 were first screened for phenotypic colistin resistance by the broth microdilution method. Twelve phenotypically colistin-resistant isolates were screened for mcr-1 to mcr-5 genes by multiplex PCR. Five of these isolates were found to carry the mcr-1 by PCR. Whole-genome sequencing of the mcr-1 carrying isolates revealed the presence of additional antimicrobial resistance genes and chromosomal gyrA and parC mutations conferring resistance to fluoroquinolones. Analysis of virulence gene content revealed 5-20 virulence genes in the isolates and two isolates were defined as avian enteropathogenic E. coli (APEC). Phylogenetic analysis based on whole-genome and multilocus sequence typing revealed that the strains were closely related to mcr-1 carrying isolates from chicken and human clinical isolates previously reported from different parts of the World. The findings further emphasize the urgent need to implement effective control programs to prevent the emergence and dissemination of colistin-resistant bacteria.