Genome-Based In Silico Analysis of the Structural and Functional Characteristics of the Type Three Secretion System (T3SS) and Core Effector Proteins in Enteropathogenic Escherichia coli (EPEC) Strains Isolated from Food-Producing Animals and Products of Animal Origin

Enteropathogenic Escherichia coli (EPEC) is a significant diarrheagenic pathotype responsible for severe gastrointestinal infections, particularly in vulnerable populations. The aim of this study is to utilize genome-based in silico analysis to study the structural and functional characteristics of the Type III Secretion System (T3SS) and its core effector proteins in EPEC strains. Representative proteins were selected, with particular interest placed on EscV and EscD as major parts of the export apparatus and the basal body, while the EspA effector protein forms the filamentous structure. Several in silico-based techniques were employed, revealing key structural proteins, core effectors, and adhesion-related proteins among the sequenced isolates. Of the 27 isolates analyzed, only 3 (11%) were found to carry LEE-encoded proteins associated with T3SS structural components (escV, escN, escD, and escU) and core effector proteins (espA, espD, espG, and eae). Structural predictions and Ramachandran plot validations suggested stability and potential functional conservation of T3SS proteins, with EscV and EspA selected for detailed 3D structural modelling. Insights into transmembrane domains, protein–protein interaction, and secondary structures were obtained, providing a comprehensive understanding of T3SS assembly and function. These findings suggest that the T3SS in EPEC consists of stable proteins that enable the system to remain functional. The structural and functional properties of the LEE genes encoding the T3SS in the EPEC pathotype represent promising targets for developing virulence blockers to disrupt the pathogenesis of a broad range of bacteria. This study is the first to report EPEC strains with functional T3SS in South Africa, emphasizing the importance of continued surveillance and molecular characterization of EPEC strains. The findings contribute to the development of targeted interventions to mitigate foodborne infections and improve public health.