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Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
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Occurrence and Genotypic Characterization of Selected Multidrug-resistant ESKAPE-E Pathogens Isolated from Integrated

Sheldon Viviers1, Loandi Richter1, Jonathan Featherston2

  • 1Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0028, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence Food Security, Pretoria 0001, South Africa.

Journal of Food Protection
|May 18, 2025
PubMed

Insights

Antimicrobial resistance (AMR) is a global threat. Multidrug-resistant bacteria, including ESBL-producers, were found on South African fresh produce farms, highlighting risks in the food chain.

Area of Science:

  • Environmental microbiology
  • Public health
  • Food safety

Background:

  • Antimicrobial resistance (AMR) is a critical global health concern.
  • Multidrug-resistant (MDR) pathogens like ESBL-producing Enterobacterales and Pseudomonas aeruginosa are priority threats.
  • Limited data exists on AMR in smallholder agricultural settings, particularly in South Africa.

Purpose of the Study:

  • To investigate the presence and characteristics of ESBL/AmpC-producing Enterobacterales and P. aeruginosa.
  • To analyze AMR profiles (phenotypic and genotypic) in these priority pathogens.
  • To assess AMR in the water-soil-plant nexus of South African smallholder fresh produce farms.

Main Methods:

  • Sampling of irrigation water, soil, and fresh produce from six smallholder farms.
  • Isolation and identification of potential MDR bacteria using selective media and MALDI-TOF MS.
  • Antimicrobial susceptibility testing (AST) against 13 antibiotic classes.
  • Whole-genome sequencing (WGS) of 20 selected isolates for genotypic AMR profiling.

Main Results:

  • ESBL/AmpC-producing isolates were detected in 17% of environmental and produce samples.
  • The highest prevalence was found in fresh produce (54%), followed by soil (31%) and water (15%).
  • Dominant species included Enterobacter spp., Klebsiella spp., Serratia spp., and Escherichia coli, exhibiting resistance to beta-lactams, aminoglycosides, and glycylcyclines. WGS revealed clinically significant AMR and virulence genes, often on mobile genetic elements.

Conclusions:

  • The study confirms the presence of ESBL/AmpC-producing MDR bacteria in the South African smallholder agricultural environment.
  • Findings underscore the potential risk associated with the informal fresh produce supply chain.
  • Data is crucial for developing targeted interventions and risk assessments to mitigate AMR spread.
Keywords:
Antimicrobial resistanceESKAPE-EFood safetyWGSWater-soil-plant-nexus

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