Analysis of Active Bacteria Persisting after Chemomechanical Procedures: An RNA- and DNA-based Molecular Study.

INTRODUCTION: Because active cells present higher abundance of ribosomal RNA (rRNA) than rDNA (rRNA genes), data obtained with rDNA-based quantitative polymerase chain reaction (qPCR) and rRNA-based qPCR (RT-qPCR) were correlated to search for active bacteria after chemomechanical procedures (CMP). In addition, the ability of both assays to detect bacteria in endodontic samples was evaluated. METHODS: Samples were taken from 40 teeth with primary endodontic infections before (S1) and after CMP (S2). DNA and cDNA (synthetized from RNA) were used as templates for qPCR using universal primers for bacteria and species-specific primers for Bacteroidaceae sp. HOT-272, Cutibacterium acnes, Selenomonas spp., and Enterococcus faecalis. RESULTS: After CMP, there was a drastic reduction in the number of total bacteria, Selenomonas spp., and E. faecalis, whereas no significant difference was observed for the levels of Bacteroidaceae sp. HOT-272 and C. acnes. The concentration of rRNA copies in S2 samples was significantly higher than the corresponding levels of rDNA for assays targeting total bacteria, Bacteroidaceae sp. HOT-272, and C. acnes (P < .05), indicating persistence of active bacteria. The rDNA-based qPCR presented low sensitivity and high specificity when compared with RT-qPCR. For most assays, samples positive for rDNA were also positive for rRNA (positive predictive value = 100%). CONCLUSIONS: CMP was effective in reducing levels but not the metabolic activity of total bacteria. Bacteroidaceae sp. HOT-272 and C. acnes were active members of the persistent community. Although less sensitive than RT-qPCR, most rDNA-based qPCR assays had a low risk of providing false-positive results in postinstrumentation samples.

Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.

INTRODUCTION: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections. METHODS: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis. RESULTS: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1). CONCLUSIONS: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.