Genomic characterization of conjugative plasmids carrying the mcr-1 gene in foodborne and clinical strains of Salmonella and Escherichia coli

Abstract

To date, the genomic characterization of foodborne bacteria carrying the mobile colistin resistance gene mcr-1 and transferability of mcr-1-carrying plasmids between wild-type bacteria have not been studied in detail. We retrospectively investigated the prevalence of mcr-1-positive Salmonella and Escherichia coli isolated from retail food products, food supply chain, and clinical samples across China in the last decade (2006–2017). The horizontal transfer of mcr-1-bearing plasmids and their complete nucleotide sequence were characterized using conjugation, S1-nuclease pulsed-field gel electrophoresis, and Southern hybridization, coupled with Illumina and Nanopore sequencing. Twelve (0.67%) mcr-1-positive strains were identified from 1789 non-duplicated isolates, including 1283 Salmonella and 506 E. coli. Eleven (21.7‰) mcr-1-positive E. coli strains were identified from the isolates collected during 2006–2017, which was significantly more prevalent than mcr-1-positive Salmonella in this period (0.78‰, 1/1283; P < 0.05). All donors (nine mcr-1-positive isolates, designated as D1–9) were multidrug resistant with diverse antimicrobial susceptibility profiles and were resistant to polymyxin B. mcr-1-carrying plasmids in donors were successfully transferred to recipients at frequencies of 4.6 × 10−2 to 6.25 × 10−4 per recipient cell. A ~33 kb IncX4-type plasmid in D1, which carried mcr-1 with the insertion sequence IS26 upstream, was effectively transferred to recipient R1. D2, D4, and their corresponding transconjugants harbored a ~60 kb IncI2-type plasmid with the insertion sequence ISApl1 upstream of mcr-1. A ~60 kb conjugative mcr-1-bearing plasmid derived from D5 also belonged to type IncI2 and contained the mcr-1 gene cassette ISEcp1-blaCTX-M-55-mcr-1-PAP2. In conclusion, mcr-1 was commonly detected in type IncI2, IncX4, and IncHI2 plasmids and mcr-1 encoding colistin resistance was successfully transferred between foodborne and clinical strains of E. coli and Salmonella isolated in China. mcr-1 gene cassettes including IS26-mcr-1-PAP2, ISAPl1-mcr-1-PAP2, and ISEcp1-blaCTX-M-55-mcr-1-PAP2 can be transferred horizontally between wild-type bacteria via conjugation. The new mcr-1 gene cassette discovered in this study provided evidence for co-transfer of mcr-1 and other antibiotic resistance genes. This finding suggests that antibiotics, other than colistin, should be used in combination for the treatment and prevention of diseases caused by foodborne pathogens. The co-transfer of mcr-1 and other antibiotic resistance genes will also enhance antibiotic resistance in foodborne pathogens.