Genetic Analysis of Plasmid-Encoded mcr-1 Resistance in Enterobacteriaceae derived from poultry meat.

Background: Colistin is classified as the highest priority and critically important antimicrobial for human medicine by the World Health Organization as it is the last resort agent for treatment of carbapenem resistant Enterobacteriaceae in humans. Additional research is necessary to elucidate the genetic structure of mcr-1 resistance genes, commonly found on plasmids, using whole genome sequencing. Objectives: The goal of this research is to map and compare the genetic characteristics of 35 mcr-1-mediated colistin resistant Enterobacteriaceae isolated from chicken meat to highlight the genetic variation of the mcr-1 containing plasmids. Methods: Sequencing was performed using Illumina HiSeq2500, Novaseq6000 and ONT's GridION. GridION data was locally base called and demultiplexed using ONT's Albacore 2.3.4 followed by Porechop 2.3. Quality filtering was performed using Filtlong 2.0. Hybrid Assembly was performed using Unicycler 4.7. Plasmids were compared to reference sequences in plasmid-refseq and pATLAS. Results: A total of 35 mcr-1 positive Enterobacteriaceae were investigated, which resulted in 34 qualitatively robust hybrid assemblies of 2 Klebsiella pneumoniae and 32 Escherichia coli. Mcr-1.1 was present in 33/34 isolates. One isolate contained an mcr-1.1-like resistance gene, due to a deletion of one codon. Two mcr-1.1 genes were located on the chromosome, while the majority of the mcr-1 genes were found on IncX4 type plasmids (n=19). Almost all plasmids identified in this study, were highly similar to plasmids found in human derived strains. Conclusions: The mcr-1.1 encoding plasmids from retail chicken show high sequence similarity to human mcr-1.1 plasmids, suggesting that this may be a contributor to the presence of colistin resistance in humans.