Genomic insight into the antibiotic-resistant determinants of Escherichia coli from small ruminants and manure in North West Province, South Africa.

INTRODUCTION

Livestock-associated Escherichia coli are important reservoirs of antimicrobial resistance and virulence determinants, yet comprehensive genomic data describing their genomic diversity and antibiotic resistance in South African small-ruminant production systems remain limited.

OBJECTIVE

Whole-genome sequencing was performed on 19 E. coli isolates recovered from sheep, goats, and manure collected from two farming systems in the North West Province, South Africa.

MATERIALS AND

METHODS

Genomic analyses revealed a dual pattern of clonal expansion and deep heterogeneity, with globally distributed sequence types (ST10, ST155) occurring alongside several novel or rarely reported STs. Comparative genomic analyses incorporating average nucleotide identity (ANI), multilocus sequence typing (MLST), in silico serotyping, antimicrobial resistance profiling, virulence characterization, and mobile genetic element analysis revealed substantial genomic diversity, comprising globally disseminated sequence types, including ST10 and ST155, together with several novel and infrequently reported lineages.

RESULTS

Although most isolates (n =17) belonged to phylogroups A and B1, the resistome was dominated by the multidrug efflux gene mdf(A) (95%) and bla TEM - 1B (58%), corresponding with high phenotypic resistance to erythromycin (74%) and ampicillin (95%), while 26% of isolates exhibited multidrug-resistant phenotypes. Genomic analysis identified 71 plasmids representing diverse incompatibility groups and mobility classes, including conjugative and mobilizable IncHI1B and IncR plasmids carrying clinically relevant resistance genes. Approximately 89% belonged to commensal lineages (A and B1), while groups D and E were each represented by a single isolate.

CONCLUSION

To our knowledge, this represents the first whole-genome sequencing-based genomic characterization of E. coli recovered from sheep and goats in South Africa, thereby expanding the known genomic diversity of livestock-associated E. coli within the country. Furthermore, data generated in this study emphasizes the necessity of ongoing genomic monitoring to track the emergence and spread of resistant E. coli, which is crucial for monitoring and mitigating potential public health risks.