Detection and Isolation of stx2e-Positive O139:H1 Shiga Toxin–Producing Escherichia coli from Surface Waters of Apulia Region (Southern Italy)

Shiga toxin–producing Escherichia coli (STEC) are important zoonotic pathogens that can disseminate through environmental water systems, yet data from Southern Italy remain scarce. The aim of this study was to investigate the occurrence and genetic characteristics of STEC isolated from surface water samples collected from rivers and lakes in the Apulia region (Southern Italy). A total of 120 samples were processed according to ISO/TS 13136:2012, followed by whole genome sequencing (WGS) for isolate confirmation and characterization. Overall, 20% of the samples were stx-positive in screening. STEC strains were isolated from 4.2% of stx-positive enrichments, corresponding to one sample out of a total of 120 (0.8%). The isolate was identified as O139:H1, carrying the stx2e subtype and belonging to sequence type ST1. Genomic analysis revealed multiple virulence-associated determinants, including the complete F18 fimbrial operon (fedA-F), hlyA, csgA, gad, chuA, yehA-D, and ompT, along with stress-resistance and tellurite-resistance genes. The strain was susceptible to all antibiotics tested. The genomic profile suggests a swine-associated lineage with multiple environmental persistence traits but limited antimicrobial resistance. The detection of a swine-associated STEC strain in surface waters highlights potential environmental dissemination pathways and underscores the importance of continued monitoring within integrated water–livestock surveillance frameworks.