Genomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans

Abstract

Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function. IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.

Keywords: Escherichia coli; IncX4; colistin; horizontal gene transfer; mcr; plasmid-mediated resistance; transfer.

FIG 1

Genetic relatedness and antibiotic resistance profiles of mcr-1.26-positive E. coli from poultry and human in Germany. (A) A maximum likelihood phylogenetic tree based on 3,722,829 SNPs was constructed with the web-based tool CSIPhylogeny 1.4 of the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) using the human clinical isolate 803-18 as reference. Background of isolate names are colored according to their phylogenetic group, which was determined by ClermonTyper (http://clermontyping.iame-research.center/). Serotype and MLST were identified by SeroTypeFinder 2.0.1 and MLST-Finder 2.0.9 of CGE. (B) Genetic antibiotic resistance profiles of isolates were obtained by using ResFinder 4.1 of CGE. The predicted location of genes in the chromosome (blue) and on plasmids (red) is shown. (C) Percentage frequency of resistance genes. Unless otherwise stated, all programs were used with the default settings.

FIG 2

Schematic representation of two mcr-1.26-harboring IncX4 plasmid prototypes. pEc141188 (below) represents the basic structure of mcr-1.26 carrying IncX4 plasmids present in 14 E. coli isolates from poultry and human. Plasmid pEc200574 (above) differs from pEc141188 by insertion of a 4,960-bp Tn2 element containing a bla_TEM-135 gene and was found in three E. coli isolates. The transposon was inserted at an intergenic TATTG sequence, resulting in the formation of 5-bp direct repeats flanking the transposon.