Genomic Evaluation of Multidrug-Resistant Extended-Spectrum β‑Lactamase (ESBL)-Producing Escherichia coli from Irrigation Water and Fresh Produce in South Africa: A Cross-Sectional Analysis

Escherichia coli, both
commensal
and pathogenic, can colonize plants and persist in various environments.
It indicates fecal contamination in water and food and serves as a
marker of antimicrobial resistance. In this context, 61 extended-spectrum
β-lactamase (ESBL)-producing E. coli from irrigation water and fresh produce from previous studies were
characterized using whole genome sequencing (Illumina MiSeq). The
Center for Genomic Epidemiology and Galaxy platforms were used to
determine antimicrobial resistance genes, virulence genes, plasmid
typing, mobile genetic elements, multilocus sequence typing (MLST),
and pathogenicity prediction. In total, 19 known MLST groups were
detected among the 61 isolates. Phylogroup B1 (ST58) and Phylogroup
E (ST9583) were the most common sequence types. The six ST10 (serotype
O101:H9) isolates carried the most resistance genes, spanning eight
antibiotic classes. Overall, 95.1% of the isolates carried resistance
genes from three or more classes. The blaCTX‑M‑1, blaCTX‑M‑14, and blaCTX‑M‑15 ESBL genes were associated
with mobile genetic elements, and all of the E. coli isolates showed a >90% predicted probability of being a human
pathogen.
This study provided novel genomic information on environmental multidrug-resistant
ESBL-producing E. coli from fresh produce
and irrigation water, highlighting the environment as a reservoir
for multidrug-resistant strains and emphasizing the need for ongoing
pathogen surveillance within a One Health context.