Chromosomally and Plasmid-Located mcr in Salmonella from Animals and Food Products in China

Abstract

This study aimed to investigate the prevalence and genomic characteristics of the colistin resistance gene mcr in Salmonella enterica in China. In total, 445 S. enterica isolates from animals and food products were screened through PCR and sequencing for the presence of mcr. The mcr genes were detected in nine Salmonella strains (2.02%), with complete mcr-1 in S. enterica serovar Indiana (n = 1) and an S. Typhimurium monophasic variant (S. 4,[5],12:i:-; n = 1), mcr-4.3 in S. enterica serovar London (n = 1), and an incomplete mcr-1 in S. Indiana (n = 6). They exhibited MIC values of 0.25 to 8 mg/L to colistin and showed resistance to multiple antimicrobial agents. Whole-genome sequencing was performed on mcr-positive Salmonella strains using Illumina HiSeq or PacBio single-molecule real-time sequencing. The complete mcr-1 gene was located on conjugative IncN1-IncHI2 plasmid and IncX4 plasmid, respectively, with high similarity to other mcr-1-bearing plasmids belonging to the same incompatibility type. Together with an additional 13 antimicrobial resistance genes, the incomplete mcr-1 was embedded in an 81,442-bp multiresistance region on the chromosome in S. Indiana YZ20MCS6. The Δmcr-1-pap2 segment and a set of tellurite resistance determinants (terYXWZABCDEF) in six S. Indiana strains were similar to other IncHI2 plasmid backbones. The mcr-4.3 gene was located on an untyped plasmid pYULZMPS10. Although low prevalence of mcr was observed in Salmonella, continuous surveillance of this gene in Salmonella is required. Plasmids play an important role in mcr transmission, and mcr-1, although incomplete, can be captured by chromosomes with the help of mobile elements. IMPORTANCE Colistin is a last-resort antibiotic for severe infections caused by multidrug-resistant (MDR) Gram-negative pathogens. Colistin resistance genes mcr, particularly mcr-1, have been found in Enterobacteriaceae around the world, mainly in Escherichia coli and Salmonella. Salmonella enterica is a major foodborne pathogen, with MDR Salmonella being considered a "Serious Threat Level pathogen" by the Centers for Disease Control and Prevention. Therefore, the prevalence of mcr in Salmonella strains must be monitored. In this study, a low mcr prevalence (2.02%) was observed in Salmonella strains from animals and food products, with plasmid-borne mcr-1 in S. enterica serovar Indiana and an S. Typhimurium monophasic variant (S. 4,[5],12:i:-) and chromosomally located mcr-1 in S. Indiana. The mcr-4.3 gene was first identified in S. enterica serovar London associated with an untyped plasmid. Although this study reports a low mcr prevalence in Salmonella, the transmission ability of mcr-positive Salmonella strains to humans via the food chain is a public health concern.

Keywords: Salmonella; chromosome; mcr-1; mcr-4.3; plasmid.

FIG 1

The insertion of mcr-1 in plasmid pYUYZMCS14-1 and chromosome of YZ20MCS6 in this study and structural comparison with related mcr-1-carrying IncHI2 plasmids. The arrows indicate the positions and the transcription directions of the genes. The delta symbol (Δ) indicates a truncated gene or mobile element.

FIG 2

Genetic structures of the multiresistance region in the chromosome of the isolate YZ20MCS6 in this study and comparison with other plasmids or chromosomes. Regions with >99% identity are shaded in gray. Resistance genes are shown in red. Genes on the chromosome of S. Indiana are shown in green. The delta symbol (Δ) indicates a truncated gene or mobile element. ISs are shown as boxes labeled with their name. Labeled vertical arrows with IS box indicate the insertion site of the IS element. Direct repeats are indicated by arrows and sequences.

FIG 3

Genetic structure of mcr-4.3 in plasmid pYULZMPS10 and comparison with other related plasmids or chromosomes. The arrows indicate the positions and the transcription directions of the genes. Regions with >99% identity are shaded in gray. Direct repeats are indicated by arrows and sequences.