Serogroups, antibiotic resistance profiles and virulence factors, of non-O157 Shiga-toxin producing Escherichia coli from ovine and caprine

Shiga toxin-producing Escherichia coli (STEC) are important zoonotic pathogens linked to foodborne illnesses and outbreaks globally, yet little is known about their prevalence and resistance profiles in small ruminants and their surrounding environment in South Africa. This study investigated the presence and antimicrobial resistance of Shiga toxin-producing E. coli (STEC) in small ruminants and their environments from 207 analyzed samples, comprising of faecal samples from sheep (114), goats (n = 58) as well as manure (n = 27) and water (n = 8). The presence of E. coli was detected using the uidA gene PCR assay, while STEC was identified using PCR assays targeting the stx genes, followed by confirmation via disk diffusion method. A total of 112 confirmed E. coli isolates were identified, with the following distribution: 57 isolates originated from sheep, 46 from goats, and 8 from manure, while no isolates were detected in water. Out of 112 confirmed E. coli isolates, PCR screening identified 26 STEC isolates, all positive for stx1 (100%) and 7.1% for stx2 genes. Serogroup analysis revealed O128 (23%) as the most common, followed by O26 (11.5%), O121 (7.6%), and O103 (3.8%), with no detection of high-risk serogroups O157, O113 or O145. Antimicrobial susceptibility testing showed high resistance against ampicillin (88.5%), erythromycin (53.8%), streptomycin (23.1%), ceftriaxone (15.3%), meropenem (11.5%) and gentamycin (3.8%). Only 11.5% of the STEC strains exhibited multidrug resistance (MDR). Genotypic profiling revealed bla _SHV (92.3%) as the most prevalent resistance gene, followed by aadA (11.5%), ampC (11.5%) as the most commonly detected antibiotic resistance genes. These findings highlight sheep and goats as potential reservoirs of pathogenic and occasionally multidrug-resistant STEC strains, reinforcing the need for integrated surveillance through a One Health framework to mitigate zoonotic risk.