Distribution and Transmission of Colistin Resistance Genes <i>mcr-1</i> and <i>mcr-3</i> among Nontyphoidal Salmonella Isolates in China from 2011 to 2020

Abstract

Mobile colistin resistance (<i>mcr</i>) genes are present mainly in plasmids and can disseminate clonally or horizontally via either plasmids or insertion sequences in different genomic locations among the <i>Enterobacteriaceae</i>. A nationwide large-scale study on <i>mcr</i> prevalence and transmission in nontyphoidal Salmonella isolates is still lacking. Here, we identified 140 <i>mcr</i>-positive Salmonella isolates out of 7,106 isolates from 29 provinces in China from 2011 to 2020. We aligned short reads to putative plasmids from long-read hybrid assemblies and predicted the plasmid backbones of non-long-read sequencing isolates to elucidate <i>mcr</i> transmission patterns. The <i>mcr-1</i> and <i>mcr-3</i> genes are transmitted on similar high-risk clones (sequence type 34 [ST34]) but through plasmids of various replicon types. Furthermore, the ban on colistin use in food animals can lead to a decrease in the <i>mcr</i>-positive Salmonella prevalence among diarrheal patients, related mainly to IncHI2A_IncHI2 plasmids. We provide a framework for plasmid data incorporation into genomic surveillance systems, contributing to a better understanding of <i>mcr</i> spread and transmission. <b>IMPORTANCE</b> Nontyphoidal Salmonella is one of four major causative agents of diarrheal diseases globally, with most cases of salmonellosis being mild. Antimicrobial treatments are required for cases of life-threatening infections, and colistin is one of the last-line antibiotics for the treatment of multidrug-resistant Salmonella infections. However, the efficacy of colistin has been compromised by the emergence of various <i>mcr</i> genes. To elucidate the transmission of <i>mcr</i> genes in Salmonella isolates, our study analyzed 7,106 Salmonella strains from 29 provinces in China from 2011 to 2020. The results showed that <i>mcr</i> genes are transmitted on similar high-risk clones (ST34) but through plasmids of various replicon types. In addition, our data illustrated that the ban on the use of colistin in food animals led to a significant decrease in <i>mcr</i>-positive isolates. Our findings offer an essential step toward a more comprehensive understanding of the spread and transmission of <i>mcr</i> genes.