Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Salmonella entericaserovar 4,[5],12:i:-, so-called Typhimurium monophasic variant, has become one of the most frequently isolated serovars both in humans and in animals all over the world. The increasing prevalence ofmcr-1-carryingSalmonellaposes significant global health concerns. However, the potential role ofSalmonella4,[5],12:i:- inmcr-1gene migration through the food chain to the human remains obscure. Here, we investigated 337Salmonellaisolates from apparently healthy finishing pigs, which is rarely studied, obtained from pig farms and slaughterhouses in China. Themcr-1gene was found in four colistin-resistantS. enterica4,[5],12:i:- isolates. Notably, all four isolates belonged to sequence type 34 (ST34) with multidrug resistance phenotype. Further genomic sequencing and antimicrobial resistance characterization confirmed thatmcrwas responsible for the colistin resistance, and the conjugation assay demonstrated that three of four isolates carriedmcr-1in IncHI2 plasmid. Importantly,mcr-1and class-1 integron were found to co-localize in two strains with IncHI2 plasmid. By collecting all themcr-1-carrying Typhimurium and monophasic variant strains across the food chain (farm animals, animal-origin food, and humans), our phylogenomic analysis of available 66 genomes, including four strains in this study, demonstrated an independent phylogenetic cluster of all eight Chinese swine-originated isolates and one human isolate. Together, this study provides direct evidence for clonal and pork-borne transmission ofmcr-1bySalmonella4,[5],12:i:- ST34 in China and highlighted a domestication pathway by acquisition of additional antimicrobial resistance determinants in Chinese ST34 isolates.