Impact of root canal preparation using two single-file systems on the intra-radicular microbiome of teeth with primary apical periodontitis

This study aimed to describe the effects of two single-file systems on the diversity of the endodontic microbiome of teeth with primary asymptomatic apical periodontitis. The root canals from single-rooted teeth with apical periodontitis were prepared using either the Reciproc Blue (RB) or the XP-endo Shaper (XPS) instrument system. The latter was followed by a supplementary step with the XP-endo Finisher (XPF) instrument. For irrigation, 5.25% sodium hypochlorite was used. Root canal samples were taken at the baseline (S1), after preparation (S2), and after the supplementary step (S3). DNA was extracted and subjected to high-throughput sequencing using the MiSeq Illumina platform. Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. The most dominant phyla in S2 were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria. The same phyla were found to dominate baseline samples and samples taken after using XPF, but with differences in the ranking of the most dominant ones. At the genus level, the most dominant genera identified after RB instrumentation were Bacteroidaceae [G-1], Fusobacterium, and Staphylococcus, while the most dominant genera after XPS instrumentation were Fusobacterium and Porphyromonas. These genera were also dominant in the initial samples. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems.
Both treatment protocols caused a measurable reduction in the root canal microbial diversity, with no significant differences between them. Most of the dominant taxa involved in the primary infection and probably in the etiology of apical periodontitis were eliminated or substantially reduced. The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus and Bacteroidaceae [G-1].