Abstract
PurposeReady-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.MethodsThe study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.ResultsBacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).ConclusionThe results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.
Highlights
Foodborne diseases associated with microbial pathogens, their toxins, or metabolites are a serious global public health problem
Taxonomic assignment of prokaryotic sequences from vended foods and environmental samples The sequence reads of length >250 bp from Illumina sequencing libraries ranged between 210,536 and 539, 981 sequences from both vended food and environmental samples
Comparison of prokaryotic diversity in vended foods and environmental food samples Prokaryotic diversity was examined within individual samples and between different samples
Summary
Foodborne diseases associated with microbial pathogens, their toxins, or metabolites are a serious global public health problem. Direct metagenome sequencing complements rRNA gene-based characterization by providing information on physiological potential of the microorganisms. Investigation of foodborne pathogens, their source, and associated risks can be done using metagenomics which provides an exhaustive sequencing depth that represents the broader microbial community in the environment (Kergourlay et al 2015). This technology has proved to be useful in the detection of microorganisms in food and has been previously used to detect Firmicutes in tomatoes (Ottesen et al 2019) and extremely halophilic archaea in food-grade salts (Henriet et al 2014). Sequencing is important in detecting and characterizing foodborne pathogens (Djenane et al 2014)
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