Escherichia coli is found in diverse environmental niches, including meat and meat products, and is known for its significance in both food safety and public health. In South Africa, whole genomic sequencing (WGS) efforts for E. coli are overwhelmingly skewed toward human isolates with limited studies conducted on non-human isolates. Therefore, the aim of this study was to use WGS to characterise generic strains of E. coli isolated from animal specimens, meat, and meat-based products in South Africa. Based on WGS analysis, a total of 35 E. coli strains were grouped into five phylogroups (A, B1, B2, C, and E), with A (46%) being the most predominant. Virulence-associated genes identified the isolates as either extra-intestinal pathogenic E. coli (69%) or intestinal pathogenic E. coli (31%) pathotypes. Twenty-three different serotypes were identified, with O101:H37 (17%), O2:H4 (17%), O6:H5 (13%), and O64:H19 (9%) being the predominant ones. Among the 19 different sequence types (STs), ST1858, ST975, and ST10 were the most prevalent (11% each). Various virulence genes, antimicrobial resistance genes, and genetic mobile elements carrying Tn2, IS26, and Tn6196 elements were detected, with the disinfectant resistance sitABCD being the most predominant. The type 1 CRISPR system which functions by storing records of previous invasions to provide immunological memory for a rapid and robust response upon subsequent viral infections was detected in all isolates, consisting of subtypes I-E (86%), I-A (57%), and I-F (11%). The findings of this study provide an insight into the genetic diversity of generic E. coli isolates from animal species, meat, and meat-based products in South Africa.

Background and Aim: Peste des petits ruminants (PPR) is an acute, extremely contagious transboundary viral disease of small ruminants with severe economic consequences, caused by PPR virus. Cost-effective and rapid diagnosis of the disease is essential for prompt management and control. This study aimed to compare the application of a commercial colorimetric loop-mediated isothermal amplification (cLAMP) kit and reverse transcriptase-polymerase chain reaction (RT-PCR) in the diagnosis of PPR in sheep and goats in Southeast Nigeria. Materials and Methods: Nasal swab samples were collected from West African Dwarf sheep and goats showing clinical signs suggestive of PPR (n=80) and those without any clinical signs (n=140) of the disease. The diagnosis was achieved through detection of PPR viral genome in the samples using a cLAMP kit and RT-PCR. cLAMP assay was done directly on nasal swab samples without ribosomal nucleic acid extraction. A set of six primers targeting the matrix gene protein was used for the cLAMP assay. Results: PPR viral genome was detected by both cLAMP and RT-PCR in 51 (63.8%) of the 80 samples from sheep and goats with signs suggestive of PPR while 14 (10%) of those without signs tested positive for PPR by both assay methods. There was a 100% agreement in the cLAMP and RT-PCR results. However, cLAMP was a faster, easier, and less expensive method compared to RT-PCR. Conclusion: The cLAMP assay demonstrates the potential for a point of care diagnosis in the field and a valuable diagnostic tool in areas with poor electricity supply as well as in a less equipped diagnostic laboratory. Since the reagents are affordable, cLAMP can be a diagnostic tool of choice in the detection and surveillance of PPR virus in countries with limited resources.

Staphylococcus aureus (S. aureus) produces an array of virulence factors (VFs), which contribute to its pathogenicity. One of the VFs is the type VII secretion system (T7SS), a protein secretion apparatus present in many Gram-positive bacteria, which plays a major role during the onset of infection. This study aimed to investigate the presence of secreted effector proteins and core structural proteins of the T7SS of S. aureus isolated from raw meat, processed meat products, and veterinary samples of food-producing animals. Whole-genome sequencing (WGS) and bioinformatics tools were employed to analyze S. aureus (n = 27) isolates. The results revealed that all 27 isolates investigated harboured various genes encoded by the T7SSb: secreted effector proteins (EsxA and EsxB) and core structural proteins (EssA, EssB, EssC, EsaA, and EsaB). The presence and absence of certain genes were observed, but overall, all these isolates harboured the major protein EssC. The EssC C-terminal found in these isolates was found to be conserved, and they clustered between the EssC1 and EssC3 variants. Ramachandran plot validations and predictions indicated the stability and likely operating conservation of T7SSb proteins. An analysis of protein–protein interactions, transmembrane domains, and secondary structures offered a thorough understanding of T7SSb assembly and how various proteins interact with each other. The results revealed that the isolates contained an array of T7SSb proteins, indicating the presence of proteins associated with various human infections, which highlights the practical application of a continuous surveillance monitoring programme and investigation of S. aureus strains.

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.