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. However, 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 STEC in small ruminants and their environments from 207 analyzed samples, comprising of faecal samples from sheep (n = 114), goats (n = 58, as well as environmental samples, including manure (n = 27) and water (n = 8) collected from goat and sheep kraals. The presence of E. coli and STEC was detected using the uidA and stx gene PCR assays, respectively. This was followed by the disk diffusion method to determine antibiotic susceptibility profiles of STEC isolates. A total of 112 confirmed E. coli isolates were identified by detecting the uidA gene, with the following distribution: 60 (53.5%) isolates originating from sheep, 46 (41.0%) from goats, and 6 (5.3%) from manure, while no isolates were detected from water samples. Out of 112 uidA PCR positive samples, n = 26 were STEC isolates which were all positive for stx1 (100%) gene, while 7.1% also harboured the stx2 gene. 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 STEC isolates exhibited multidrug resistance (MDR). Genotypic profiling revealed blaSHV (92.3%) as the most prevalent resistance gene, followed by aadA (11.5%) and ampC (11.5%). 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.