Genetic analysis of plasmid-encoded resistance in Enterobacteriaceae derived from poultry meat in the Netherlands.

BACKGROUND

Colistin is classified as the highest priority and critically important antimicrobial for human medicine by WHO 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 resistance genes, commonly found on plasmids, using WGS.

OBJECTIVES

To map and compare the genetic characteristics of 35 -mediated colistin-resistant Enterobacteriaceae isolated from chicken meat to highlight the genetic variation of the containing plasmids.

METHODS

Sequencing was performed using Illumina HiSeq2500, Novaseq6000 and ONT's GridION. GridION data was locally basecalled 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 with reference sequences in plasmid-RefSeq and pATLAS.

RESULTS

A total of 35 positive Enterobacteriaceae were investigated, which resulted in 34 qualitatively robust hybrid assemblies of 2 and 32 . was present in 33/34 isolates. One isolate contained an like resistance gene, due to a deletion of one codon. Two genes were located on the chromosome, while the majority of the genes were found on IncX4 type plasmids (=19). Almost all plasmids identified in this study were highly similar to plasmids found in human-derived strains.

CONCLUSIONS

The -containing plasmids from retail chicken show high sequence similarity to human plasmids, suggesting that this may be a contributor to the presence of colistin resistance in humans.