Description of Antimicrobial-Resistant Escherichia coli and Their Dissemination Mechanisms on Dairy Farms

SIMPLE SUMMARY: There is little information about antimicrobial resistance and the transmission of this resistance in dairy cattle. The aim of this work is to use cutting-edge technology (whole genome sequencing) to characterize antimicrobial resistance of bacteria (Escherichia coli) retrieved from the manure of dairy cattle and to determine how this resistance spreads among the E. coli population on dairy farms in Québec, Canada. It detects some resistance genes for antimicrobials considered to be of high priority and critical importance to human medicine. Some of these genes are situated close to each other as well as in the vicinity of some elements for transfer between bacteria. This suggests that bacteria can share these critical antimicrobial resistance genes on dairy farms. Furthermore, the same bacterium was found on farms located up to more than 100 km apart, suggesting transmission across dairy farms. An understanding of this dissemination mechanism will allow for the elaboration of fighting strategies against these resistant bacteria. ABSTRACT: Despite its importance in veterinary medicine, there is little information about antimicrobial resistance (AMR) and its transmission in dairy cattle. The aim of this work is to compare AMR phenotypes and genotypes in resistant Escherichia coli and to determine how the resistance genes spread among the E. coli population on dairy farms in Québec, Canada. From an existing culture collection of E. coli isolated from dairy manure, a convenient selection of the most resistant isolates (a high level of multidrug resistance or resistance to broad-spectrum β-lactams or fluoroquinolones) was analyzed (n = 118). An AMR phenotype profile was obtained for each isolate. Whole genome sequencing was used to determine the presence of resistance genes, point mutations, and mobile genetic elements. In addition, a subset of isolates from 86 farms was taken to investigate the phylogenetic relationship and geographic distribution of the isolates. The average agreement between AMR phenotypes and genotypes was 95%. A third-generation cephalosporin resistance gene (bla(CTX-M-15)), a resistance gene conferring reduced susceptibility to fluoroquinolones (qnrS1), and an insertion sequence (ISKpn19) were detected in the vicinity of each other on the genome. These genes were harbored in one triplet of clonal isolates from three farms located >100 km apart. Our study reveals the dissemination of resistant E. coli clones between dairy farms. Furthermore, these clones are resistant to broad-spectrum β-lactam and fluoroquinolone antimicrobials.