Molecular characterization and detection of antibiotic resistant genes of bacteria isolated from yoghurt in Port Harcourt Metropolis, Nigeria

Currently, molecular identification is replacing the conventional method because of its precision and reliability whereas the effectiveness of antibacterial treatments has continuously declined due to antimicrobial resistance (AMR). This study aimed to identify the bacterial isolates; phenotypically and molecularly as well as detect the resistant genes after susceptibility testing of the isolates obtained from yoghurt samples. Standard microbiological techniques and molecular analysis were applied on both samples (commercial and home-made yoghurt) for species validation. Forty-four (44) bacterial species were identified, phenotypically belonging to three (3) genera; Bacillus, Staphylococcus and Lactobacillus and an additional genus Bifidobacterium emerged from molecular analysis. The microbial load of the yoghurt samples was not statistically significant at (p≥0.05). A sensitivity test on the species was carried out using Kirby-Bauer disc diffusion method with some standard antibiotics. The results revealed that Bacillus and Staphylococcus species were resistant to ampicillin and augmentin (100%) but susceptible to ofloxacin and gentamicin respectively. Lactobacillus spp. were susceptible to ofloxacin and ceftazidime (100%), and resistant to ampicillin, augmentin, and ciprofloxacin (100%). The six most resistant species were molecularly identified as S. aureus CP019117, S. epidermidis AB68833, B. megaterium KC246043, B. cereus NC004722, Lactobacillus casei NC008526 and Bifidobacterium lactis CP003941. Resistant bacteria with mecA gene are S. aureus and S. epidermidis and those with ampC gene are Bifidobacterium lactis and Lactobacillus casei. However, neither gene was found in the genome of any Bacillus species. However, the data also revealed that the bacterial species in home-made yoghurt samples were negative for mecA and ampC resistant genes but positive in the commercial samples. These genes contributed to the bacterial isolates' high levels of multidrug resistance (MDR). The presence of resistant genes in bacterial species from commercial yoghurt samples remains a challenge for food safety. Therefore, good manufacturing practice, proper hygiene and sanitation is hereby advocated to avoid serious emerging foodborne illnesses.