Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets

Abstract

The use of colistin in food-producing animals favors the emergence and spread of colistin-resistant strains. Here, we investigated the occurrence and molecular mechanisms of colistin resistance among E. coli isolates from a Mexican piglet farm. A collection of 175 cephalosporin-resistant colonies from swine fecal samples were recovered. The colistin resistance phenotype was identified by rapid polymyxin test and the mcr-type genes were screened by PCR. We assessed the colistin-resistant strains by antimicrobial susceptibility test, pulse-field gel electrophoresis, plasmid profile, and mating experiments. Whole-Genome Sequencing data was used to explore the resistome, virulome, and mobilome of colistin-resistant strains. A total of four colistin-resistant E. coli were identified from the cefotaxime-resistant colonies. All harbored the plasmid-borne mcr-1 gene, which was located on conjugative 170-kb IncHI-2 plasmid co-carrying ESBLs genes. Thus, high antimicrobial resistance rates were observed for several antibiotic families. In the RC2-007 strain, the mcr-1 gene was located as part of a prophage carried on non-conjugative 100-kb-plasmid, which upon being transformed into K. variicola strain increased the polymyxin resistance 2-fold. The genomic analysis showed a broad resistome and virulome. Our findings suggest that colistin resistance followed independent acquisition pathways as clonal and non-genetically related mcr-1-harboring strains were identified. These E. coli isolates represent a reservoir of antibiotic resistance and virulence genes in animals for human consumption which could be potentially propagated into other interfaces.

First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh

“…Although the location of all ARGs couldn't be confirmed due to short length sequencing, this study identified a 288 kb megaplasmid of highly transferable IncHI2 family that carries ARGs conferring resistance to aminoglycosides {aadA2, ant (3")-IIa, aph(3')-IIa, aph(3")-Ib, aph(6)-Id}, phenicols (cmlA1), sulfonamides (sul1, sul3), tetracyclines (tetA, tetR) and trimethoprims (dfrA15). Occurrence of MDR with mcr-1 E. coli has been reported earlier [9,47], however, rats carrying these types of resistance determinants on plasmids are firstly reported in this study to the best of our knowledge. Occurrence of MDR E. coli carrying ARGs on horizontally transferable elements is worrisome and imposes a potential threat of transferring and disseminating these resistance determinants to human and animals through contaminated food, water and environment.…”

“…Occurrence of MDR with mcr-1 E . coli has been reported earlier [ 9 , 47 ], however, rats carrying these types of resistance determinants on plasmids are firstly reported in this study to the best of our knowledge. Occurrence of MDR E .…”

Editorial for the Special Issue: Colistin Resistance—The Need for a One Health Approach

“…The isolates belonged to three different serotypes and phylogroups. All the strains were phenotypically resistant to multiple antimicrobials and carried several resistance and virulence genes [ 11 ].…”