Genomic profiling of Escherichia coli strains from food producing animals and animal derived food products in South Africa

Abstract

Escherichia coli is one of the most extensively studied bacterial species worldwide due to its remarkable adaptability, genomic diversity, and zoonotic potential. The increasing prevalence of antimicrobial resistance (AMR) among E. coli strains represents a growing public-health concern, particularly in countries such as South Africa where the consumption of animal-derived food products is widespread. However, E. coli is not exclusively associated with foods of animal origin only; it is also commonly detected in non-animal derived products such as fresh produce and water, highlighting the importance of investigating multiple sources. This study specifically focuses on isolates from animal derived food products and does not attempt to give a full representation of E. coli’s ecological distribution within South Africa. This study employed whole-genome sequencing (WGS) and comparative genomic approaches to characterize E. coli isolates from animals, meat, and meat products, focusing on phylogenetic assignment, virulence gene repertoire, mobile genetic elements, plasmid content, AMR determinants, and Type III Secretion System (T3SS) components. Isolates included in this study originated from food-producing animals and animal-derived products from species such as poultry, bovine, ovine and porcine, these products included processed meat, meat itself and faecal material from some of these species. Genomic DNA was extracted from isolates confirmed as E. coli and further sequenced using Illumina sequencing platforms. This was followed by quality assessement of the sequences, genome assembly and annotation. In this study, downstream analysis included serotyping of these isolates, determination of antimicrobial resistance, virulence genes, plasmid detection, and characterisation of CRISPR-Cas system. Comparative genomic analysis in this study included phylogenetic analysis of South African strains with publicly available African genomes. Based on WGS analysis of 35 isolates, five phylogroups (A, B1, B2, C, and E) were identified, with phylogroup A predominating (46%). Virulence profiling revealed that 69% of isolates were extra-intestinal pathogenic E. coli (ExPEC) and 31% intestinal pathogenic (InPEC), encompassing 23 serotypes and 19 sequence types (STs), the most common being ST1858, ST975, and ST10. A wide array of virulence and AMR genes, including those associated with transposons Tn2, IS26, and Tn6196, was detected, while the metal transport system resistance operon sitABCD was ubiquitous. Type I CRISPR systems were observed in all isolates, dominated by subtypes I-E (86%) and I-A (57%). In-silico analysis of T3SS revealed that only three isolates (11%) carried LEE-encoded structural genes (escV, escN, escD, escU) and effector proteins (espA, espD, espG, eae). Structural modeling confirmed the stability and functional conservation of EscV and EspA, suggesting an intact and potentially functional T3SS apparatus in localized EPEC strains the first such report from South Africa. Comparative genomic analysis of 159 E. coli ST10 genomes from 19 African countries revealed extensive intra-lineage diversity, with 71% of isolates being multidrug resistant and 29% carrying bla_CTX-M-15. Plasmid replicon analysis identified widespread IncFIB and ColRNAI plasmids strongly associated with AMR determinants. Collectively, these findings highlight the evolutionary plasticity, virulence potential, and One Health significance of E. coli lineages circulating in Africa, underscoring the urgent need for integrated genomic surveillance and targeted interventions to mitigate foodborne and zoonotic transmission risks.