Antibiotic Resistance Genes in Periodontitis

Antibiotic resistance is recognized today as one of the most serious global threats to public health. Worldwide, it has been documented that in 2019, 1.27 million deaths were directly attributable to bacterial antibiotic resistance, and 4.95 million deaths were associated with it. Bacteria can acquire antibiotic resistance not only through spontaneous mutations but also through horizontal gene transfer (HGT). HGT refers to the transfer of resistance genes between different bacterial species. This transfer occurs through transformation, conjugation, or transduction, and via mobile genetic elements (MGEs) such as plasmids, transposons, and bacteriophages. The excessive and inappropriate use of antibiotics is one of the main triggers for the emergence of antibiotic resistance. When antibiotics become ineffective, bacteria cannot be suppressed, and the dissemination of resistance genes between bacterial populations accelerates through HGT. This leads to the emergence of super-resistant bacterial strains and a reduction in the efficacy of antibiotic therapies. Periodontitis is a multifactorial, chronic inflammatory disease characterized by the destruction of periodontal tissues supporting the tooth. The prevalence and rate of progression of periodontitis are closely related to complex interactions between periodontopathogenic bacteria and host immune cells. In periodontal health, Gram-positive bacteria such as Actinomyces and Streptococcus dominate the dental plaque biofilm, forming a balanced ecosystem in homeostasis with host cells. Disruption of this homeostasis leads to environmental changes that cause a dysbiotic shift in the biofilm composition. The subgingival biofilm constitutes the primary etiological factor of periodontal disease. The management of periodontal diseases mainly relies on the removal of subgingival biofilm. Mechanical therapy is generally effective in eliminating biofilm and resolving inflammation. However, in certain patient groups (e.g., young adults with rapidly progressing disease) and clinical situations (e.g., acute periodontal abscesses or necrotizing periodontal diseases accompanied by systemic manifestations), mechanical therapy alone may be insufficient to achieve successful outcomes. As stated in the 2017 Classification of Periodontal and Peri-implant Diseases and Conditions and in the European Federation of Periodontology (EFP) S3-level Clinical Practice Guideline for the Treatment of Stage I-III Periodontitis, adjunctive antibiotic therapy is beneficial in such cases. From this perspective, while antibiotics play an important role in periodontal therapy, periodontal diseases themselves may also contribute to the global rise in antimicrobial resistance (AMR). Possession of a specific antibiotic resistance gene (ARG) by a bacterium indicates that the bacterium has the ability to protect itself against, or neutralize, the corresponding antibiotic. This information reflects the bacterial genotype associated with antibiotic resistance and is of great importance for evaluating the antimicrobial resistance (AMR) profile.

In this study, the total genomic DNA of microorganisms isolated from the subgingival biofilms of periodontitis and healthy individuals will be sequenced, and through bioinformatic analyses, the microbial diversity, genetic composition, antibiotic resistance gene profiles, and associated mobile genetic elements (MGEs) of the subgingival microbiome will be comprehensively characterized using shotgun metagenomic techniques. Thus, the study will not only reveal the presence of resistance genes in periodontitis but also their potential for mobility and HGT. The shotgun metagenomic approach surpasses classical 16S rRNA analyses by enabling the identification of microbial communities at both species and gene levels. In this context, the sequencing data obtained will be compared against up-to-date databases such as CARD, RGI, ARGs-OAP, MobileElementFinder, PlasmidFinder, ICEberg, and ISfinder, to evaluate the distribution, diversity, and association of resistance genes with MGEs within the microbiota. Within the scope of this project, subgingival plaque samples from 25 healthy and 25 periodontitis subjects attending Istanbul University Faculty of Dentistry will be collected. After DNA isolation, shotgun metagenomic analyses will be performed to determine the presence, genetic organization, and HGT-mediated dissemination potential of ARGs. The sequencing data will be analyzed using bioinformatic methods to investigate both the bacterial potential for spreading resistance genes via HGT and possible increases in this transfer potential within the dysbiotic flora.

The results obtained from this project will contribute to understanding the relationship between periodontal diseases and antibiotic resistance, providing scientific evidence that supports rational antibiotic use in periodontal therapy.

The findings of this study will enhance our understanding of the role of the oral microbiota in resistance mechanisms and may assist in developing new strategies to improve the efficacy of antibiotic treatments.

In this way, the project aims to promote more conscious and evidence-based antibiotic use in the management of periodontal diseases.