Abstract
Ready-to-eat (RTE) foods play a significant role in everyday life and have been
considered to be a reservoir of antibiotic-resistant bacteria (AR bacteria), which pose
a direct threat to public health, however, their potential underlying microbiological risks
remain poorly understood. In this study, an assembly-based metagenomic approach
was used to profile bacterial communities and ARGs associated with RTE food
products in 18 RTE samples (8 RTE vegetable products, RTE fruit products, 3 RTE
dairy products and 3 RTE processed meat) from Gauteng Province, South Africa.
Sequencing was carried out using Illumina HiSeq technology, a short-read highthroughput
sequencing platform, data analysis was conducted using metagenomics
pipelines and bioinformatics tool, offering comprehensive insight into microbial
diversity, associated ARGs and virulence genes. The study revealed a bacterial
community dominated by Proteobacteria, Firmicutes and Bacteroidetes. Opportunistic
pathogenic and spoilage bacteria such as Staphylococcus, Bacillus, Clostridium,
Campylobacter and Pseudomonas were detected significantly. Functional annotation
uncovered valuable pathways involved in selenium-amino acid biosynthesis, pyruvate
fermentation, fatty acid biosynthesis and L-methionine biosynthesis. Additionally, AMR
gene analysis indicated the presence of ARGs, with the most common ARGs genes,
detected conferring resistance to tetracycline, efflux pump, and aminoglycosides,
notably the study also detected high-risk virulence genes including those encoding for
motility (e.g flgH), adhesion (e.g vfr and rpos) and biofilm (e.g algl). The study’s
findings have significant implications for public health. Additionally, this study
advances our understanding of the antibiotic resistome, microbiome, and virulence
genes in RTE foods, laying the foundation for future research on RTE foods.