Genetic insights into antimicrobial resistance and virulence characteristics of Salmonella enterica isolated from Nile tilapia sourced from retail markets in Thailand

BMC Microbiol. 2025 Nov 25;25(1):777. doi: 10.1186/s12866-025-04451-0.

Abstract

Background: Antimicrobial-resistant Salmonella enterica in aquaculture represents a significant public health concern due to its potential transmission through the food chain. Despite these concerns, there is a notable lack of comprehensive genomic characterization of S. enterica isolates from Nile tilapia in Thailand. This study aimed to evaluate the prevalence, antimicrobial resistance (AMR) profiles, and genetic diversity of S. enterica isolated from retail-sourced Nile tilapia (Oreochromis niloticus) between May and October 2023.

Methods: A total of 714 Nile tilapia specimens comprising liver, kidney, meat, gill, mucus, lung, and intestine tissues were collected from fish purchased at retail markets in Thailand. Salmonella isolation and identification were performed using standard microbiological methods following ISO 6579-1:2017, and serotyping was conducted using the Kauffmann-White scheme. Antimicrobial susceptibility testing was carried out using the agar dilution method in accordance with CLSI guidelines. The whole genome sequencing was performed on 14 multidrug-resistant isolates using Illumina short-read technology to characterize their genetic resistance and virulence profiles.

Results: The prevalence of S. enterica was 15.4%, with the highest rates observed in gill (40.9%) and mucus (26.5%) samples. Thirty-five serovars were identified, with Escanaba, Kentucky, and Othmarschen being the most frequently detected. Resistance to oxytetracycline (33.6%), tetracycline (16.0%), and ampicillin (12.8%) were prevalent, and 19.2% of isolates exhibited multidrug resistance (MDR). Although extended-spectrum beta-lactamase (ESBL)-producing isolates accounted for only 2.4%, concerns persist regarding their increasing global prevalence. WGS of 14 MDR isolates identified over 20 resistance genes, including blaTEM-1B, blaCTX-M-55, qnrS1, and tet(A), as well as efflux pump systems (mdsABC and mdtK) and various virulence factors.

Conclusions: These isolates were classified into nine sequence types (STs), several of which have been associated with human infections. The findings underscore the necessity of stringent antimicrobial regulations and improved aquaculture practices to mitigate AMR transmission and enhance food safety.

Keywords: Salmonella enterica; Antimicrobial resistance; Nile tilapia; Virulence factors.

MeSH terms

  • Animals
  • Anti-Bacterial Agents / pharmacology
  • Cichlids* / microbiology
  • Drug Resistance, Multiple, Bacterial / genetics
  • Fish Diseases* / epidemiology
  • Fish Diseases* / microbiology
  • Microbial Sensitivity Tests
  • Salmonella Infections, Animal* / epidemiology
  • Salmonella Infections, Animal* / microbiology
  • Salmonella enterica* / drug effects
  • Salmonella enterica* / genetics
  • Salmonella enterica* / isolation & purification
  • Salmonella enterica* / pathogenicity
  • Seafood / microbiology
  • Thailand
  • Virulence / genetics
  • Virulence Factors / genetics
  • Whole Genome Sequencing

Substances

  • Anti-Bacterial Agents
  • Virulence Factors