Metagenomic Profiling and Natural Product-Based Control of Antibiotic-Resistant Streptococcus Species in Gut Microbiome of Diarrhea-Associated Children

The threat of antibiotic resistance extends beyond established pathogens. Recent research highlights the concerning role of normal gut bacteria in holding and potentially spreading antibiotic resistance genes. This phenomenon poses a significant risk to human and animal health worldwide. In this study, we aimed to understand the antibiotic resistance profile of gut bacteria and determine the abundance of bacteria at the species level based on metagenomic analysis and investigate control methods. Fecal samples were collected from 150 pediatric diarrhoea patients from Kushtia 250-bed General Hospital, Bangladesh and cultured in anaerobic conditions. The presence of antibiotic resistance was analyzed by the disk diffusion method, and the microbial profiling was plotted by metagenomic analysis. The abundant antibiotic-resistant strain was identified and controlled using natural compounds. Antibiotic-resistant bacteria against the tested 10 antibiotics were prevalent in 0-6-month old children samples and followed by 7-12-month-old children. In 25-30-month old children samples, bacteria were resistant against all the antibiotics except Doxycycline, and Levofloxacin. Based on metagenomic analysis Firmicutes is the most abundant phylum in antibiotic resistance samples. The presence of Streptococcus was observed only in antibiotic-resistant samples whereas Lactobacillus, Lysinibacillus, Vagococcus, Pseudomonas, Lentibacillus, and Corynebacterium have a higher tendency of susceptibility than resistance. Antibiotic-resistant Streptococcus was isolated on Streptococcus selection agar and controlled by aqueous extract of Cloves. Although human gut microbes perform various health benefits, multiple drug resistance among human gut bacteria will be a great threat to human health. Hence, alternative sources of antibiotics expanded the consciousness of using antibiotics as a treatment. Natural products can be used as therapeutic agents to control multiple drug-resistant bacteria.