Occurrence and Genotypic Characterization of Selected Multidrug-resistant ESKAPE-E Pathogens Isolated from Integrated...

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.