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.
Highlights
Colistin represents the last line of therapeutic options against multidrug-resistant strains of Enterobacterales
This study reports the molecular and genomic traits of mcr-1-harboring E. coli from piglets
Our results show that colistin resistance followed independent acquisition pathways, but a common conjugative 170-kb plasmid was identified in the majority of isolates
Summary
Colistin represents the last line of therapeutic options against multidrug-resistant strains of Enterobacterales. Plasmid-borne mcr genes have been found in a variety of plasmid types such as IncI2, IncHI2, IncX4, IncP, IncF and the less common IncY [3]. These plasmids are transferable with a broad host range, which could explain the widespread of mcr genes among different bacterial species [4]. Ten variants of the mcr gene have so far been described [5], but the most widespread is the mcr-1 gene [6] This gene has been identified in isolates from numerous sources including humans, food, farms and wild animals [7,8]. Mcr genes are found in association with other antimicrobial resistance genes, usually extended-spectrum-ß-lactamases (ESBL) and carbapenemases, highlighting the emergence of pan-drug resistant Enterobacterales [6]
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