Bacterial Food Contaminants in Vended Fast Foods, Soil and Water in Embu Town, Kenya

Abstract

Ready to eat fast food vending business has grown exponentially however, the microbiological safety of most of these fast foods is questionable. Despite the cholera outbreak in Embu in 2017, diminutive information exists on waterborne and foodborne illness outbreaks resulting from bacterial pathogens in Embu Town and the nearby Kangaru Market. Thus this study aimed to isolate and characterize bacterial food contaminants in the vended fast foods and their surrounding environment in Embu Town and nearby Kangaru Market. Bacterial isolates were isolated from; fried fish, African sausages, roasted meat, samosa, fries, vegetable salads, soil and water. Antibiotic susceptibility testing was done using the Kirby-Bauer method. DNA was extracted from pure isolates using the phenol-chloroform method. The 16S rRNA and resistant genes were amplified with the respective primers. Taxonomy was assigned to each Operational Taxonomic Units using BLAST. Sequence alignment and construction of the phylogenetic tree were done using MEGA X. Total community DNA was 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 was performed according to Illumina sequencing protocol. Sequence analysis was done using QIIME2 while Analysis of similarity (ANOSIM) test, based upon Bray-Curtis distance, Non-metric Multidimensional Scaling (NMDS), redundancy analysis (RDA) as well as Hierarchical clustering of the samples, were carried out using the R programming language. Taxonomic groups were derived from the number of reads assigned to each taxon at all ranks from domain to species using the taxa summary.txt output from the QIIME2 pipeline. Antibiotic resistance of the isolates was; chloramphenicol 90%, cefotaxime 84.29%, nalidixic acid 81.43%, tetracycline 77.14%, amoxicillin 72.86%, gentamycin 48.57%, streptomycin 32.86% and trimethoprim + sulphamethoxazole 30%. Isolate KMP337, exhibited significantly high antibiosis against S. aureus recording an average inhibition of diameter mean and standard error (SE)16.33±0.88mm respectively at P = 0.001. Polymerase chain reaction detected the presence of resistance genes; tet (A), bla TEM, strB, dfr (1), bla Amp, and Flor genes. The isolates clustered in five main genera namely Bacillus, Paraclostridium, Lysinibacillus, Virgibacillus, and Serratia all having similarity of above 90%. The OTUs were distributed among twenty-three bacterial phyla across the samples with the most abundant belonging to Proteobacteria (52.81%), Firmicutes (31.16%), Bacteroidetes (8.00%) and Lentisphaerae (0.001%). The OTUs were shared among archaea as follows; Candidatus nitrososphaera (83.89%) and Nitrososphaera (11.43%). Lactobacillus perolens, Pseudomonas spp., Clostridium spp., and Bacillus cereus were detected in abundance across the samples. Potential pathogens in risk group 2 including Rickettsia spp. and Brucella spp., Coxiella spp. in risk group 3 were detected. Uncultured Candidatus koribacter sp, Candidatus microthrix sp. and Candidatus solibacter sp. were detected in food. This study confirmed the presence of antibiotic-resistant foodborne potential pathogens in vended fast foods and the soil in Embu Town and Kangaru Market. The study, therefore calls for continuous monitoring of bacterial status and hygienic handling of vended foods. The detection of potential pathogens calls for stringent hygiene measures in food vending operations, especially in Kangaru Market.