Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011–2016

Abstract

The emergence of plasmid-mediated colistin resistance (<i>mcr</i> genes) threatens the effectiveness of polymyxins, which are last-resort drugs to treat infections by multidrug- and carbapenem-resistant Gram-negative bacteria. Based on the occurrence of colistin resistance the aims of the study were to determine possible resistance mechanisms and then characterize the <i>mcr</i>-positive <i>Escherichia coli</i>. The research used material from the Polish national and EU harmonized antimicrobial resistance (AMR) monitoring programs. A total of 5,878 commensal <i>E. coli</i> from fecal samples of turkeys, chickens, pigs, and cattle collected in 2011-2016 were screened by minimum inhibitory concentration (MIC) determination for the presence of resistance to colistin (R) defined as <i>R</i> > 2 mg/L. Strains with MIC = 2 mg/L isolated in 2014-2016 were also included. A total of 128 isolates were obtained, and most (66.3%) had colistin MIC of 2 mg/L. PCR revealed <i>mcr-1</i> in 80 (62.5%) isolates recovered from 61 turkeys, 11 broilers, 2 laying hens, 1 pig, and 1 bovine. No other <i>mcr</i>-type genes (including <i>mcr-2</i> to -<i>5</i>) were detected. Whole-genome sequencing (WGS) of the <i>mcr-1</i>-positive isolates showed high diversity in the multi-locus sequence types (MLST) of <i>E. coli</i>, plasmid replicons, and AMR and virulence genes. Generally <i>mcr-1.1</i> was detected on the same contig as the IncX4 (76.3%) and IncHI2 (6.3%) replicons. One isolate harbored <i>mcr-1</i>.<i>1</i> on the chromosome. Various extended-spectrum beta-lactamase (<i>bla</i> _{<i>SHV</i>-12}, <i>bla</i> _{<i>CTX</i>-<i>M</i>-1}, <i>bla</i> _{<i>CTX</i>-<i>M</i>-15}, <i>bla</i> _{<i>TEM</i>-30}, <i>bla</i> _{<i>TEM</i>-52}, and <i>bla</i> _{<i>TEM</i>-135}) and quinolone resistance genes (<i>qnrS1</i>, <i>qnrB19</i>, and chromosomal <i>gyrA, parC</i>, and <i>parE</i> mutations) were present in the <i>mcr-1</i>.<i>1</i>-positive <i>E. coli</i>. A total of 49 sequence types (ST) were identified, ST354, ST359, ST48, and ST617 predominating. One isolate, identified as ST189, belonged to atypical enteropathogenic <i>E. coli.</i> Our findings show that <i>mcr-1</i>.<i>1</i> has spread widely among production animals in Poland, particularly in turkeys and appears to be transferable mainly by IncX4 and IncHI2 plasmids spread across diverse <i>E. coli</i> lineages. Interestingly, most of these <i>mcr-1</i>-positive <i>E. coli</i> would remain undetected using phenotypic methods with the current epidemiological cut-off value (ECOFF). The appearance and spread of <i>mcr-1</i> among various animals, but notably in turkeys, might be considered a food chain, and public health hazard.