Metagenomic analysis of total microbial diversity and antibiotic resistance of culturable microorganisms in raw chicken meat and mung sprouts (Phaseolus aureus) sold in retail markets of Mumbai, India

Raw chicken meat and ready-to-eat sprouts are potential sources of food-borne infections. Development and spread of antibiotic resistance (AR) in microflora associated with food is a major health concern. In this study, we employed culturable and non-culturable methods to characterize microflora associated with chicken meat and mung. Pathogens belonging to Enterobacteriaceae were dominant in the culturable set. Rare species like Citrobacter amalonaticus, Kluyvera georgiana, Kurthia gibsonii and Staphylococcus hominis were isolated and metagenomic study revealed overall good species richness in both food types, Firmicutes and Gammaproteobacteria were dominant phyla in chicken meat and sprouts respectively. Common food-borne and opportunistic pathogens like Campylobacter, C. perfringens, Streptococcus, Shewanella, Pseudomonas, Aeromonas hydrophila, Staphylococcus, E. coli, Acinetobacter, Enterobacter, Klebsiella were detected and 18% of the genera were common to both food types. We observed high AR bacterial count (5 to 9 log CFU/g) in the microflora. Fifty AR isolates per food type were identified with high multiple AR index of 0.3-0.9.