Antibiotic Resistant Gene Prevalence In Primary And Secondary Endodontic Infections: A Whole-Metagenome Shotgun Based Study

Abstract

PURPOSE: The purpose of this study was to assess the prevalence of antibiotic resistant genes in primary and secondary endodontic infections using whole-metagenome shotgun sequencing. This study was also used to determine if a difference exists between the counts per million of antibiotic resistant genes present in primary versus secondary endodontic infections. MATERIALS AND METHODS: Twenty-five samples from patients with primary root canal infections, and twenty samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analyzed with whole-metagenome shotgun sequencing at a depth of 15–20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. We profiled a manually curated list of antibiotic resistant genes in our metagenomic data using the KEGG BRITE database (https://www.genome.jp/brite/ko01504). To assess if a significant difference exists between infections belonging to primary and secondary endodontic infections, a Mann-Whitney U test non-parametric test was used. P-value was two tailed and significance was determined at P<0.05. RESULTS: Thirty-seven total samples yielded high-quality DNA, 21 and 16 samples that belonged to primary and secondary infection samples, respectively. The most prevalent antibiotic resistant genes present included the metallo-beta-lactamase family protein, MFS transporter (DHA1 family, bicyclomycin/chloramphenicol), multidrug resistance protein (MATE family), membrane fusion protein (multidrug efflux system), and multiple antibiotic resistance protein. The bacteria encoding for antibiotic resistant genes that have the highest prevalence in primary and secondary endodontic infections included Eubacterium infirmum, Tannerella forsythia, Psuedopropionibacterium propionicum, Dialister pneumosintes, Prevotella Denticola, and Selenomonas sputigena. Mann-Whitney U analysis showed no significant difference between counts per million of primary and secondary endodontic infections (P = 0.6532). CONCLUSIONS: Numerous antibiotic resistant genes are prevalent and encoded for in both primary and secondary endodontic infections. No significant difference was found between the prevalence in counts per million of antibiotic resistant genes between the microbial composition in cases with primary or secondary endodontic infections.