Life sciences · Journal article

Genomic epidemiology of Salmonella Typhimurium in Guizhou, China (2019–2023): high prevalence of MDR, plasmid-associated resistance, and shared genomic lineages

Frontiers in Microbiology · September 9, 2026

Preliminary Why this matters to you Expert discussion

Early or partial results. Treat as a signal, not a conclusion.

AI Summary

This is a surveillance and genomic characterization study of 103 clinical Salmonella Typhimurium isolates from Guizhou Province (2019–2023), documenting high prevalence of multidrug resistance (100% during 2019–2021), emergence of XDR phenotypes, and regional clonal expansion. The work describes resistance mechanisms and plasmid-associated ARGs but is descriptive rather than analytical, offering no intervention comparison or causal evidence; it informs regional epidemiology and supports a public health surveillance recommendation.

What was studied

Retrospective genomic epidemiology study. Clinical Salmonella Typhimurium isolates (n=103) from nine cities in Guizhou Province, China.. n = 103. Nine cities in Guizhou Province, China..

Key findings

Multidrug resistance (MDR) was universal (100%) during 2019–2021, with extensively drug-resistant (XDR) isolates emerging in 2020. Substantial resistance to first-line antibiotics: ciprofloxacin 16.5%, ceftazidime 19.4%, cefotaxime 36.9%, azithromycin 12.6%. Whole-genome sequencing identified 61 antimicrobial resistance genes (ARGs) and six distinct point mutations.

Safety

Clinical outcomes (morbidity, mortality, treatment failure) are not reported; only resistance profiles are characterized.

Who this may help

Clinicians and public health authorities in affected regions should be aware of high prevalence of multidrug resistance and fluoroquinolone/cephalosporin resistance in S. Typhimurium, informing empirical therapy decisions. The identification of shared genomic lineages across provinces and species suggests food supply chain and cross-regional transmission risks, supporting integrated surveillance under a One Health framework.

Plain-language summary

A descriptive genomic epidemiology study of 103 clinical isolates with phenotypic and WGS characterization, lacking a comparator or intervention and providing surveillance data rather than hypothesis testing or clinical outcomes.

Study design

As stated by the source record.

MethodsPhenotypic and whole-genome sequencing (WGS) analysis of 103 clinical S. Typhimurium isolates collected from nine cities in Guizhou Province over five years (2019–2023). Antimicrobial susceptibility testing (phenotypic), WGS-based ARG detection, plasmid replicon typing, molecular typing (ST and cgST), and phylogenetic analysis were performed. Genotype–phenotype correlation was assessed using Kappa statistics.

DesignRetrospective genomic epidemiology study

PopulationClinical Salmonella Typhimurium isolates (n=103) from nine cities in Guizhou Province, China.

Sample size103

SettingNine cities in Guizhou Province, China.

Reported figures

Quoted from the source exactly as published.

Sample size103

Multidrug resistance prevalence (2019–2021)100%

Ciprofloxacin resistance16.5%

Ceftazidime resistance19.4%

Cefotaxime resistance36.9%

Azithromycin resistance12.6%

Total antimicrobial resistance genes (ARGs) identified61

Point mutations identified6

Clinical bottom line

Caveats

No comparator or control group; this is a descriptive epidemiological survey without hypothesis testing or causal inference.
Clinical outcomes (morbidity, mortality, treatment failure) are not reported; only resistance profiles are characterized.
Sampling strategy and potential selection bias (e.g., whether isolates represent all S. Typhimurium in the region or only certain patient populations) are not detailed.
No temporal trend analysis or statistical testing of year-to-year changes in resistance prevalence is provided.

Evidence assessment

Graded across the dimensions that decide whether you should act, each from what the source actually supports. There is no single score, and where a dimension was not assessed it says so.

Study design

moderate

Integrated phenotypic and genomic analysis of clinical isolates; observational, no experimental arm.

Directness

limited

Genomic and resistance profiling; no clinical outcomes, patient data, or treatment response measured.

Consistency

moderate

Resistance genotypes correlated well with phenotypes for six antibiotic classes (Kappa 0.48–0.74).

Risk of bias

insufficient

Source describes collection from nine cities across five years but does not detail sampling strategy or potential selection bias.

Sample adequacy

moderate

103 isolates collected across nine cities over five years; adequate for descriptive epidemiology but modest for robust inference.

Source abstract

Salmonella Typhimurium ( S. Typhimurium) is a leading cause of bacterial gastroenteritis worldwide, and its escalating antimicrobial resistance (AMR) poses a critical threat to global public health. Nevertheless, epidemiological and genomic data for this pathogen in Guizhou Province remain limited. We integrated phenotypic and genomic analyses of 103 clinical S. Typhimurium isolates, collected from nine cities between 2019 and 2023, to characterize their genetic backgrounds, resistance mechanisms, and evolutionary dynamics. The isolates exhibited persistently high resistance to conventional antibiotics. Multidrug resistance (MDR) was universal (100% during 2019–2021), with extensively drug-resistant (XDR) isolates emerged in 2020. Substantial resistance to first-line antibiotics was also observed, including ciprofloxacin (16.5%), ceftazidime (19.4%), cefotaxime (36.9%), and azithromycin (12.6%). Whole-genome sequencing (WGS) identified 61 antimicrobial resistance genes (ARGs) and six distinct point mutations. Efflux pump-associated genes were widely distributed, and ARGs conferring tetracyclines and sulfonamides were detected at high frequencies. Resistance genotypes correlated well with phenotypes for azithromycin, ceftazidime, ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, and tetracycline ( Kappa: 0.48-0.74). Twenty plasmid replicons were detected, with IncF (24.3%), IncI1-I (15.5%), and IncHI2 (13.6%) being the most prevalent. Notably, ARGs associated with resistance to critically important antibiotics (such as qnr variants, bla CTX – M and bla CMY –2, and mphA/mrx ) were frequently predicted to locate on plasmid-associated contigs. Plasmid diversity expanded significantly over the five-year period, particularly in economically developed cities. Molecular typing identified ST19 and its subtypes, cgST121877 (30.1%) and cgST59516 (12.6%), as the dominant clones, suggesting pronounced regional clonal expansion. Furthermore, phylogenetic analysis revealed close genetic relatedness between Guizhou clinical isolates and human- and livestock-derived isolates from other Chinese provinces. These findings highlight the cross-regional and cross-species circulation of shared genomic lineages, suggesting complex ecological networks that may involve the food supply chain. Implementing an integrated “One Health” surveillance strategy is critical to track and limit the circulation of these resistant lineages and mitigate the associated public health threat.

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Limei WuGe ZhuDeyu LiYanmin LiuLv YouXiaoyu Wei