Genetic epidemiology and plasmid-mediated transmission of mcr-1 by Escherichia coli ST155 from wastewater of long-term care facilities

Abstract

Long-term care facilities (LTCFs) for older people play an important and unique role in multidrug-resistant organism transmission. Herein, we investigated the genetic characteristics of mobile colistin resistance gene (mcr-1)-carrying Escherichia coli strains isolated from wastewater of LTCFs in Shanghai. Antimicrobial susceptibility test was carried out by agar dilution methods. Whole-genome sequencing and plasmid sequencing were conducted, and resistance genes and sequence types of colistin in E. coli isolates were analyzed. Core genome multilocus sequence typing (cgMLST) analysis was performed by the Ridom SeqSphere+ software. Phylogenetic tree through the maximum likelihood method was constructed by MEGA X. Out of 306 isolates, only 1 E. coli named ECSJ33 was found, and the plasmid pECSJ33 from ECSJ33 harbored the mcr-1 gene that was located with 59,080 bp belonging to IncI2 type. The plasmid pECSJ33 was capable of conjugation with an efficiency of 2.9 × 10^-2. Bioinformatic analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. Moreover, the cgMLST analysis revealed that ECSJ33 belongs to different lineages from those reported from previous E. coli strains but shared high similarity to NCTC11129 in cluster 11. The phylogenetic tree revealed MCR-1 of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Our study firstly reports detection of genome sequence of a multidrug-resistant mcr-1-harboring E. coli ST155 from wastewater of LTCF source in China. The data may prove that the plasmid pECSJ33 belongs to food origin and help to understand the antimicrobial resistance mechanisms and genomic features of colistin resistance under One Health approach.IMPORTANCEOne Escherichia coli named ECSJ33 was found from wastewater of a long-term care facility (LTCF) and the plasmid pECSJ33 from ECSJ33 harbored the mobile colistin resistance gene (mcr-1) that was located with 59,080 bp belonging to IncI2 type, which was capable of conjugation with an efficiency of 2.9 × 10^-2. This paper firstly reports an mcr-1-carrying E. coli strain ST155 isolated from LTCF in China. Comparative genomics analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. The phylogenetic tree revealed MCR-1 protein of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Therefore, the pECSJ33 could be considered as food-origin transmission mcr-1-harboring plasmid.

Keywords: Escherichia coli ST155; long-term-care facility; mcr-1; plasmid; wastewater.

Fig 1

Geographical locations of the sample sites in this study. The sites with negative results were indicated with triangle, while sites with positive results were shown in red. The maps were created using ArcGIS 10.3 software.

Fig 2

Linear comparison of complete plasmid sequences of plasmid E. coli pECSJ33 (this study), pHNGDF93 from E. coli GDT6F93 (GenBank accession no. MF978388), pHXH-5 from E. coli HXH-5 (GenBank accession no. MH202956), pK19EC149 from E. coli pK19EC149 (GenBank accession no. CP050290), pSH13G1582 from Salmonella enterica subsp. enterica serovar Typhimurium strain SH13G1582 (GenBank accession no. MH522412), and pZJ3920-3 from E. coli ZJ3920 (GenBank accession no. CP020548). The arrows represent the position and transcriptional direction of theopen reading frames (ORFs). Resistance gene (mcr-1) is indicated by the red arrow, plasmid replication proteins are indicated in blue, plasmid stability proteins are highlighted in pink arrows, and type IV secretion system genes are indicated by light blue arrows.

Fig 3

Map of mcr-1-harboring plasmid pECSJ33. The mcr-1 gene is marked in red. The figure was created using SnapGene Viewer software.

Fig 4

Phylogenetic analysis. (A) Minimum spanning tree constructed on the basis of cgMLST allelic genes of 101 MCRPEC strains. Each circle depicts an allelic profile based on sequence analysis of 3,179 cgMLST genes. The length of the connecting lines represents the number of target genes with different alleles. Each circle within the tree represents a cgMLST type, with diameters scaled to the number of isolates belonging to that type. Colors represent different isolation countries. Closely related genotypes (<10 alleles difference) are shaded in the same node, and clusters are numbered consecutively. (B) Maximum likelihood phylogenetic tree of 101 MCRPEC strains based on the core genome. The red dashed box indicates ECSJ33 strain.

Fig 5

Phylogeny of 58 MCR-1 proteins of E. coli origin retrieved from the NCBI database. Using amino acid sequences from one E. coli MCR-1 protein in this study (ECSJ33), the BLAST search tool (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 30 September 2023) was used to retrieve homologous sequences of MCR-1 and MCR-1-like proteins from the NCBI database. MCR-1 and MCR-1-like proteins of E. coli containing LptA and others were among the sequences categorized. Using aligned MCR-1 sequences from ClustalW, the maximum likelihood method of MEGA X was used to create a phylogenetic tree.