Emergence and Genomic Features of a mcr-1 Escherichia coli from Duck in Hungary

Abstract

Plasmids carrying high-risk resistance mechanisms in pathogenic E. coli have gained particular attention in veterinary medicine, especially since the discovery of the colistin resistance gene, mcr-1. Here, we provide the first evidence of its emergence and describe the complete mcr-1 plasmid sequence of a multi-resistant avian pathogenic E. coli (APEC) strain from waterfowl in Hungary. Whole-genome sequencing analysis and core-genome MLST were performed to characterize the genome structure of the mcr-1 plasmid and to reveal the phylogenetic relation between the Hungarian duck strain Ec45-2020 and the internationally circulating mcr-1-positive E. coli strains from poultry and humans. Results showed that plasmid pEc45-2020-33kb displayed a high level of genome identity with mcr-1 plasmids of IncX4 type widespread among human, animal and food reservoirs of enteric bacteria of public health. The mcr-1-positive E. coli strain Ec45-2020 belongs to the ST162 genotype, considered as one of the globally disseminated zoonotic genotypes of MDR E. coli. In accordance with international findings, our results underline the importance of continuous surveillance of enteric bacteria with high-risk antimicrobial resistance genotypes, including neglected animals, such as waterfowls, as possible reservoirs for the colistin resistance gene mcr-1.

Keywords: colistin resistance; core genome MLST; mcr-1 Escherichia coli; multiresistance; plasmid genome; waterfowl; whole-genome sequencing.

Figure 1

Phylogenetic diversity and geographical distribution of mcr-1-positive E. coli strains with origin from poultry (2016 and 2020). The Minimum Spanning Tree was generated to represent the phylogenetic relation among 114 E. coli strains from poultry based on the ST type, namely on the polymorphism of seven housekeeping genes. Nodes containing multiple strains are demarcated by grey lines. Red dotted circles indicate the STs corresponding to the duck isolates of mcr-1-positive E. coli. Distance lines change from black to dotted grey as the phylogenetic distance between the strains increases. The thickness of the distance line is inversely proportional to the distance value.

Figure 2

Core genome diversity of common ST lines of mcr-1-positive E. coli from poultry and humans. The Neighbor Joining Tree showing the genomic diversity of 238 E. coli strains was calculated based on the polymorphism of 2138 target genes of the core genome. Core genes were identified by blasting all genome sequences against the reference strain E. coli K-12 MG1655 (GenBank accession no. NC_000913).

Figure 3

Genomic features of acquired resistance and virulence and their distribution among the three resistance and hybrid plasmids. The sequence positions of the listed genes are indicated by subscripts.

Figure 4

Comparison of complete linear plasmid sequences to pEc45-2020-33kb. The plasmid set was selected from the top 100 BLAST hits which showed 100% query coverage and >95% pairwise identity. For each strain, GenBank accession numbers are indicated in parentheses.