Molecular identification of vertebrate sources and potential zoonotic pathogens in the meat value chain from selected vendors in Nairobi, Kenya

Abstract

The steady increase in the utilization of meat products has led to a rise in demand as well as its market price. Substitution of meat from animal species of higher commercial value with those from cheaper or undesirable species occurs often, posing ethical, religious, and dietary concerns. In Nairobi and Naivasha, there have been reports of bushmeat and undeclared species sold to unsuspecting customers. The aim of the study was to identify the vertebrate sources of meat sold to consumers in Nairobi hence determining if there was any species substitution in the meat value chain; and also, to detect potential pathogens in the meat sold to consumers. A total of 115 meat samples were obtained randomly from butcheries in Burma Market, Nairobi, and its surrounding areas. Additionally, seven goat samples were obtained from Kiamaiko as controls. Extraction of DNA from these samples was done using the ISOLATE II Genomic DNA extraction kit (Bioline, UK) and determination of species and bacterial screening carried out. Furthermore, ninetynine meat samples similarly obtained from Naivasha butcheries and stored at -80°C were also analyzed for presence of bacterial pathogens, making the total number of samples 221. Species identification was done using high-resolution melting (HRM) analysis of the PCR products. Three mitochondrial DNA markers, cytochrome oxidase subunit 1 (CO1), cytochrome b (cyt b), and 16S rRNA genes were targeted to identify vertebrate species. Presence of selected bacterial zoonotic pathogens was evaluated through analysis of HRM of PCR products targeting the genes bcsp31, secYIV, PL3 and IS1111 for Brucella spp., pathogenic Leptospira spp., Bacillus anthracis and Coxiella burnetii respectively. Additionally, sequencing of PCR amplified products using universal 16S rRNA was utilized to screen for more bacterial contaminants. The study detected incidence of species substitution in the meat value chain, with 15/115 samples collected in Nairobi found to be substituted. Presence of zoonotic bacteria that pose a risk to individuals involved in the meat value chain was also detected with 27/221 of the samples being positive for pathogenic Brucella, and 1/221 of the samples being positive for Leptospira interrogans. None of the samples were positive for Bacillus anthracis or Coxiella burnetii. Using the universal 16S rRNA gene primers allowed the amplification of food-borne pathogens including Lactococcus garvieae, Clostridium spp. and Aeromonas caviae in 3% of the samples, where 7/221 samples were found to have bacteria that are enteropathogenic or enterotoxin producing. These findings reveal that there may be loopholes in the meat value chain that could place consumers at risk of allergic reactions due to undeclared meat species, and to public health because of the zoonotic and foodborne bacterial pathogens present. However, no correlation could be found between species substitution and pathogens.