The Multi-Antibiotic Resistance Profile and Phylogenetic Analysis of Bacteria Using 16S rRNA Gene Sequencing and Genotyping Technology

Background: The global surveillance and profiling of the multi-antibiotic-resistant strains of bacteria have been reported by the World Health Organization in 2024 among the top priority threats facing global public health. Aim: To determine the multi-antibiotic resistance profile and phylogenetic analysis of bacteria using 16S rRNA gene sequencing and genotyping technology. Methods: The bacterial strains were used from the stocks of the routine culturing in the general microbiology laboratory in the Department of Applied Biology, University of Sharjah; these are: Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Streptococcus pyogenes. The 16S rRNA gene sequences and the phylogenetic genotyping diagnosis were determined followed by determination of the multi-resistance profile of the tested strains using 2 levels of sensitivity testing protocols; diffusion well and VITEK-2 automated system. Three multi-resistance control strains were used for quality assurance. Results: The phylogenetic diagnosis was determined using the international sequences library available in the public domain of the NCBI Gene/Bank, USA. Strains were genotyped with 99.9% homology and diagnostic positions on the phylogenetic trees for the strains of E. coli, P. aeruginosa isolates, K. pneumoniae, and S. pyogenes, respectively. The multi-antibiotic resistance profiles were as follows: E. coli 12.5% (E1), P. aeruginosa 37.5% (F1), P. aeruginosa 31.25% (H1), P. aeruginosa 31.25% (G1), P. aeruginosa 37.5% (B2), K. pneumoniae 6.25% (A1), K. pneumoniae 50% (C1), K. pneumoniae 6.25% (D1), K. pneumoniae 6.25% (D2), S. pyogenes 0% (L1), for the E. coli, P. aeruginosa, K. pneumoniae isolates, S. pyogenes, respectively. Conclusion: The results show the multi-antibiotic resistance profile of the tested strains and its phylogenetic genotyping analysis which will improve surveillance of the infectious diseases and molecular diagnosis.