Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023

Abstract

Background: The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.

Methods: A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.

Results: Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was bla_TEM-1 (54.9%), and bla_CTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, bla_NDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, bla_CTX-M , mcr-1.1, and bla_NDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.

Conclusion: The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.

Keywords: Salmonella; antimicrobial resistance genes; extensively drug-resistant; plasmid; whole-genome sequencing.

Figure 1

Antimicrobial resistance (AMR) phenotypes of 51 XDR Salmonella isolates. (A) The antibiotic resistance profiles of XDR Salmonella isolates were visualized using an UpSet plot. In the combination matrix positioned beneath the primary bar chart, individual columns corresponded to distinct AMR phenotypic profiles. Each colored dot within these columns represented resistance to a specific antimicrobial agent, with unique color coding different antimicrobial. The vertical bar chart displayed the total number of isolates exhibiting particular resistance combinations, while the horizontal bar chart displayed the prevalence of resistance for each antimicrobial agent. (B) Pie chart depicted the distribution of XDR Salmonella isolates from nine cities in Guizhou province. (C) Bar plot showed the detection rates of XDR Salmonella isolates from 2019 to 2023.

Figure 2

Analysis of serovars, STs, and antimicrobial resistance of 51 XDR Salmonella isolates. (A) Serovar prediction and MLST of 51 XDR Salmonella isolates. (B) The heatmap depicted the distribution of antimicrobial resistance across different serovars. The shades of color corresponded to the number of antimicrobial resistance isolates. Dark green indicated a high resistance rate, while white denoted the absence of resistance in that serovar.

Figure 3

Antimicrobial resistance determinants among 51 XDR Salmonella isolates. (A) The distribution of ARGs and associated amino acid mutations, with corresponding genetic elements listed on the left vertical axis. The adjacent bar chart quantified their percentages, stratified by antimicrobial class through color-coded categorization. (B) Multidrug resistance genetic determinants present gene targets along the left margin. The accompanying visualization employs chromatic differentiation to demonstrate the proportional representation of MDR-associated genetic elements within the study.

Figure 4

The prevalence of genetic determinants of antibiotic resistance in the top four common serovars of XDR Salmonella.

Figure 5

Distribution of ARGs and associated amino acid mutations located on chromosomes and plasmids of 51 XDR Salmonella isolates, targeting specific antimicrobial agents. Notably, 18 multidrug resistance genes were all located on chromosomal DNA, which did not show in this figure.

Figure 6

Phylogenetic analysis of 51 XDR Salmonella isolates using core genome MLST. The ML tree was constructed based on cgMLST profiles, with branch colors representing distinct serovars. Antimicrobial resistance phenotypes were depicted using square markers: filled blue squares indicated positive resistance phenotypes, while unfilled blue squares indicated susceptible isolates. The rightmost panel illustrated plasmid carriage and resistance gene distribution, where pink squares represented concurrent presence of both plasmids and resistance genes. Numeral within squares indicated the quantity of resistance genes corresponding to specific antibiotic classes.