One Health approach investigating Shiga toxin-producing Escherichia coli serotypes from human stool specimens and cattle run-off water samples in South Africa

Abstract

Shiga toxin-producing Escherichia coli (STEC) are known for producing cytotoxins called Shiga toxins and are prevalent in cattle. Data regarding the prevalence of STEC serotypes in South Africa is lacking. This study investigated the prevalence and genomic characteristics of clinical and environmental serotypes of STEC in South Africa, using the One Health approach. Forty-four STEC isolates were collected from a private health diagnostic laboratory and 30 run-off water samples from 10 beef abattoirs and 20 cattle feedlots. Genomic analysis involved multiplex polymerase chain reaction assays for screening Shiga toxin, O-antigen, and virulence genes. Genetic relatedness of isolates was investigated using a repetitive extragenic palindromic polymerase chain reaction assay, guiding the selection of isolates for WGS. The stx2 gene [43.18% (19/44)] was most prevalent, followed by the stx1 gene [34.09% (15/44)]. One isolate tested positive for both stx1 and stx2. The most prevalent serotype was O26 [29.55% (13/44)], followed by O157 [11.36% (5/44)]; both implicated in past outbreaks. Genes associated with severe illness in humans, including: stx2a, stx2c, stx2d, stx2f, eae and ehxA, were detected. Genetic diversity was apparent among isolates, except for two closely related isolates from human stool specimens. Hybrid strains containing extraintestinal pathogenic E. coli and other diarrhoeagenic E. coli virulence genes were detected in two isolates. Sequence type (ST) 14855, ST300, ST730 and ST5989, previously unreported in South Africa, were identified. Forty percent (4/10) of isolates harboured antimicrobial resistance (AMR) genes, including: strA, strB, sul2, tetA, tetB and dfrA. All isolates harboured multidrug-resistance-associated plasmids from the Inc-family. These results highlight the heterogeneity, genomic plasticity and propensity STEC to acquire AMR and virulence traits, increasing the bacteria’s potential to cause severe illness in humans. Farm-to-plate-to-hospital surveillance systems need to be implemented in South Africa to develop strategies to curb the spread of AMR and virulent strains of STEC.