Molecular Characterization
and Phylogenetic Insights into Pathogenic Bacteria isolated from Endodontic Infections
Panda Asha Kiran, Maity Sudipta and Barik Bibhuti Prasad
Res. J. Biotech.; Vol. 20(12); 177-183;
doi: https://doi.org/10.25303/2012rjbt1770183; (2025)
Abstract
Endodontic infections are polymicrobial in nature and often involve opportunistic
and drug-resistant pathogens. Accurate identification and molecular characterization
of these bacteria are essential for guiding targeted therapeutic strategies and
understanding their evolutionary relationships. Infected root canal samples were
aseptically collected from patients undergoing root canal treatment or retreatment
in Berhampur City, India. Three predominant bacterial isolates: Staphylococcus aureus
(BEB1), Klebsiella pneumoniae (BEB2) and Salmonella enterica (BEB3), were identified
based on morphological, biochemical (catalase, coagulase, oxidase) and molecular
criteria. Genomic DNA was extracted and the 16S rRNA gene was amplified and sequenced.
Sequences were submitted to the NCBI GenBank database. BLAST analysis determined
sequence homology and phylogenetic trees were constructed using Neighbor-Joining,
Maximum Likelihood, UPGMA and Maximum Parsimony methods in MEGA 12. RNA secondary
structure predictions were performed using LocARNA 1.5.2.
Sequence analysis revealed >99% identity with reference strains in GenBank. Phylogenetic
reconstructions consistently clustered BEB1, BEB2 and BEB3 with their respective
species clades supported by high bootstrap values (≥98%). Comparative RNA secondary
structure analysis demonstrated conserved motifs across isolates, with minor variations
in loop and stem regions, suggesting potential functional divergence. These findings
provide insights into the evolutionary adaptation of endodontic pathogens in the
studied population. This study offers the comprehensive molecular and phylogenetic
characterization of pathogenic bacteria from endodontic infections in Berhampur
city, India. The integration of 16S rRNA gene sequencing, phylogenetic analysis
and RNA secondary structure modelling enhances our understanding of the genetic
diversity and evolutionary patterns of these pathogens, laying foundation for improved
diagnostic and therapeutic approaches in endodontics.
