Whole-Genome Sequencing of Escherichia coli O18ab:H11 from South African Beef: Antimicrobial Resistance, Virulence, and a Rare Sequence Type

Antimicrobial-resistant Escherichia coli in food systems represents a growing public health concern, yet whole-genome sequencing (WGS)-based surveillance of beef-associated E. coli in South Africa remains limited. This study applied WGS to comprehensively characterise the antimicrobial resistance (AMR) profile, virulence gene repertoire, sequence type, and serotype of an E. coli isolate recovered from retail beef in KwaZulu-Natal Province, South Africa, and to contextualise these findings within the broader African E. coli population through comparative genomic analysis of 397 publicly available E. coli genome sequences retrieved from the NCBI SRA. The isolate was recovered by classical microbiological methods, confirmed by MALDI-TOF MS, and whole-genome-sequenced on the PacBio Onso platform. In silico serotyping assigned the genome to serotype O18ab:H11. MLST under the Achtman seven-locus scheme assigned the genome to ST7106, a sequence type with no prior record in South Africa. The isolate carried the intrinsic β-lactamase gene blaEC-15 (reported as chromosomal in the literature), conferring narrow-spectrum resistance to aminopenicillins, alongside an acquired resistome comprising aadA1, tet(B), and sat2, conferring resistance to aminoglycosides, tetracyclines, and streptothricin; no ESBL or carbapenemase genes were detected. The virulence gene repertoire—encompassing type 1 fimbriae (fimA–I), curli fibres (csgA–G), the E. coli common pilus (ecpRABCDE), enterobactin iron-acquisition genes, hlyE, and the invasion genes ibeB and ibeC—indicates colonisation capacity, but ibeB, ibeC, and hlyE showed no clinical enrichment relative to carriage genomes, and the isolate showed no close genomic relationships with any clinical genome; a definitive extra-intestinal pathogenic E. coli (ExPEC) pathotype assignment is therefore not supported. PathogenFinder returned a pathogenicity probability of 0.944 (532 pathogen-associated protein families detected), without in vivo corroboration. Comparative analysis identified a pan-resistome of 97 unique AMR genes across the 398 genomes, including blaCTX-M-15 (59.0%) and blaNDM-5 (49.5%), predominantly among clinical genomes. Pan-genome analysis revealed an open genomic structure (α=0.194; 16,578 gene clusters), and core-genome phylogenetics confirmed the beef-derived isolate as a genetically distinct lineage (minimum pairwise SNP distance: 1629 SNPs). These findings demonstrate the presence of a genomically distinct, potentially pathogenic E. coli lineage in the South African beef supply and highlight the importance of integrating WGS into routine food safety and AMR surveillance frameworks across the region.