Serotype Is Associated With High Rate of Colistin Resistance Among Clinical Isolates of Salmonella

Abstract

To investigate the prevalence, probable mechanisms and serotype correlation of colistin resistance in clinical isolates of Salmonella from patients in China, Salmonella isolates were collected from fecal and blood samples of patients. In this study, 42.8% (136/318) clinical isolated Salmonella were resistant to colistin. MIC distribution for colistin at serotype level among the two most prevalent serotypes originating from humans in China indicated that Salmonella Enteritidis (83.9% resistance, 125/149) were significantly less susceptible than Salmonella Typhimurium (15.3% resistance, 9/59, P < 0.01). mcr genes and mutations in PmrAB confer little for rate of colistin resistant Salmonella isolated from human patients. Phylogenetic tree based on core-genome single nucleotide polymorphisms (SNPs) was separately by the serotypes and implied a diffused distribution of MICs in the same serotype isolates. Relatvie expression levels of colistin resistant related pmr genes were significantly higher in non-mcr colistin resistant S. Typhimurium than in colistin sensitive S. Typhimurium, but no discernable differences between colistin resistant and sensitive S. Enteritidis, indicating a different mechanism between colistin resistant S. Typhimurium and S. Enteritidis. In conclusion, colistin susceptibility and colistin resistant mechanism of clinical isolated Salmonella were closely associated with specific serotypes, at least in the two most prevalent serotype Enteritidis and Typhimurium. We suggest clinical microbiology laboratory interpreting Salmonella colistin MIC results in the serotype level.

Keywords: Salmonella enterica; clinical isolates; colistin susceptibility; phylogenetic analysis; pmr genes; serotype.

FIGURE 1

Number of isolates and MIC distribution of different serotypes of Salmonella. “Other serotypes” presents serotypes except for Enteritidis and Typhimurium.

FIGURE 2

Maximum parsimony tree of the whole-genome sequenced 136 clinical Salmonella isolates. MICs (mg/L) and sequence types of colistin among different serotype Salmonella isolates were shown. Maximum parsimony tree were generated based on core-genome SNPs by kSNP 3.0. Isolates with different serotypes are indicated in the inner ring with different colors. Colistin MICs in mg/L are shown, along with corresponding mcr-1 gene and pmrAB mutations known to be associated with phenotypic resistance. For the description of colistin susceptibility, resistance corresponds to MIC > 2 mg/L and susceptible corresponds to MIC ≤ 2 mg/L.

FIGURE 3

Zoomed-in maximum parsimony tree showing the Enteritidis serotype sub-clade of the clinical Salmonella isolates. Colistin MICs in mg/L and sequence types are shown. For the description of colistin susceptibility, resistance corresponds to MIC > 2 mg/L and susceptible corresponds to MIC ≤ 2 mg/L.

FIGURE 4

Zoomed-in maximum parsimony tree showing the Typhimurium and monophasic variant of Typhimurium (Salmonella 4,[5],12:i:-) serotypes sub-clade of the clinical Salmonella isolates. Colistin MICs in mg/L and sequence types are shown. For the description of colistin susceptibility, resistance corresponds to MIC > 2 mg/L and susceptible corresponds to MIC ≤ 2 mg/L.

FIGURE 5

Relative expression levels of pmrC, pmrD, pmrE and pmrHFJKLM operon in colistin resistant and sensitive isolates of serotype Typhimurium (A) and Enteritidis (B). Gene expression levels of each target gene were identified and compared with 16s rRNA expression levels of each isolates. Relative gene expression levels of colistin sensitive (S) group and colistin resistant (R) group in serotype Typhimurium and Enteritidis were compared using p-values calculated by Statistical Package for the Social Sciences (SPSS) using rank-sum tests, respectively (*P < 0.05, **P < 0.01).