Supplementary file 1_Genomic insight into the antibiotic-resistant determinants of Escherichia coli from small ruminants and manure in North West Province, South Africa.docx

Introduction<p>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.</p>Objective<p>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.</p>Materials and methods<p>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.</p>Results<p>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.