Impact of an Enhanced Infection Control Protocol on the Microbial Community Profile in Molar Root Canal Treatment: An in Vivo NGS Molecular Study

Introduction Recent findings demonstrated that 1-year cone-beam computed tomography–based outcomes of molar root canal treatment were improved through an enhanced infection protocol (EnP), when compared with a current best-practice standard infection control protocol (StP). The EnP comprised measures to reduce iatrogenic contamination from direct and indirect contact surfaces, including the replacement of the rubber dams, gloves, files, all instruments, and surface barriers before root canal obturation. The aim of this study was to investigate the effect of such an EnP on resident microbiome present after chemomechanical instrumentation and the protocol ability in reducing iatrogenic contamination in molar teeth during root canal treatment. Methods Molar teeth were block-randomized to receive treatment under EnP or StP. To compare the differential effect of the protocol on the identity of bacteria present, 150 matched DNA extracts from 75 molar teeth samples (StP, n = 39; EnP, n = 36) were evaluated. Samples were taken before (S1) and after (S2) chemomechanical preparation and were subjected to next-generation sequencing of the V3-V4 region of the 16S rRNA gene before bioinformatical identification using the HOMD oral microbiome database and downstream taxonomic processing, providing measures of richness and diversity of bacteria and significant bacterial taxa during chemomechanical instrumentation and the effect of the 2 treatment groups. Results Eighty-eight microbial taxa were significantly more abundant in StP S2 samples, including endodontically relevant contaminants taxa as Actinomyces, Cutibacterium, and Haemophilus. The S2 samples demonstrated fewer residual bacterial species in the EnP group, with 26.8 observed species compared with 38.3 in the StP. Reduced diversity and richness measures were noted in the EnP pre-obturation samples compared with the StP in OTU, Chao1, and ACE indices (P ≤ .05). Differential microbial identities between S1 and S2 samples and protocols demonstrated that the previously observed increased effectiveness of the EnP protocol was likely to prevent recontamination or de novo contamination of the root canal space during treatment. Conclusions The implemented EnP resulted in a specific reduction of microbial taxa often associated with recontamination or iatrogenic contamination, suggesting the basis for improved infection control measures during root canal treatment.