A critical analysis of research methods and experimental models to study the root canal microbiome

Bacterial genera in the fluids from apical periodontitis-related radicular cysts: An observational study

AIM

This study aimed to evaluate bacteriome profiles (diversity, composition and relative abundances of bacterial genera) of the fluids from apical periodontitis (AP)-related radicular cysts (RCs).

METHODOLOGY

This observational study included 29 patients with AP and RC with complete sample triplets (supragingival plaque, cryopulverized tooth and cystic fluid). The bacteriome profiles of each matrix as well as of negative controls (NCs) were examined using 16S rRNA amplicon sequencing.

RESULTS

Bacteriome profiles of cystic fluids differed from NCs in 79% of cases. The number of distinct amplicon sequence variants and Shannon index detected in cystic fluids and cryopulverized teeth were significantly lower than in paired supragingival plaque samples. Gram-negative genera and anaerobic genera were more abundant in cystic fluids than in paired cryopulverized teeth or their supragingival plaques. The relative abundances of the genera Prevotella_7/Prevotella, Fusobacterium and Porphyromonas were higher in cystic fluids than in paired cryopulverized teeth and NCs; their relative abundances dominated (>20%) in individual cystic fluids. Also, DNA from the genus Fretibacterium was significantly more commonly found in cryopulverized teeth and cystic fluids than in supragingival plaque samples. The relative abundances of this gram-negative bacterial genera in cryopulverized teeth differed from NCs; the difference from cystic fluids was borderline insignificant.

CONCLUSIONS

Although the alpha-diversity in the cystic fluids is much lower compared to supragingival plaques, most cystic fluids are not sterile. DNA from specific anaerobic gram-negative bacterial genera dominated the fluids from AP-related RCs.

Microbiota of Healthy Dental Pulp Under the Omics Loupe

This study aims to contribute to the understanding of the dental pulp microbiome through metataxonomic analysis of pulp tissues from clinically healthy impacted third molars in 17 patients. Samples from coronal pulp, outer radicular dentin, and negative controls were included. Each sample was spiked with a known bacterial standard. Sequencing of the 16S rRNA V3-V4 region revealed similarity in bacterial taxonomic profiles. The bacterial DNA was detected in all pulp samples, primarily originating from reagent contaminants. Although some oral taxa appeared more abundant in pulp than in dentin or controls, contaminant species overwhelmingly dominated. Most of the extracted DNA was of human origin, rather than bacterial. Our findings question the concept of a core microbiome in healthy pulp and highlight the critical need for rigorous controls in pulpal microbiome studies.

A Methodological Study on Microbial In Vivo Sampling Methods of Root Canal Microbiota for Next-Generation Gene Sequencing Analysis

INTRODUCTION

The aim was to evaluate the suitability of paper points or endodontic nickel-titanium files to sample microorganisms for in vivo investigation of endodontic microbiota by 16S ribosomal DNA (rDNA) sequencing.

METHODS

Forty-five patients presenting clinical and radiological signs of apical periodontitis were recruited for sampling, giving their written informed consent. Glide paths were assessed using C-Pilot Files and K-Files under electronic root canal length control under aseptic conditions. Microbial samples were taken from 84 root canals in duplicate, the first sample with a sterile paper point (size 15), the second with a sterile file (size 20/.06). After DNA extraction, the hypervariable region V4 of the bacterial 16 S rRNA gene was amplified and sequenced (Illumina MiSeq). Sequencing data were trimmed with Cutadapt and exact amplicon sequence variants generated by DADA2. Taxonomy was assigned based on the Human Oral Microbiome Database (eHOMD). Statistical analysis of diversity parameters comprised Wilcoxon signed-rank tests and permutational analysis of variance (PERMANOVA). Compositional differences were evaluated by differential abundance analysis (DESeq2). Microbial contamination during the sampling process and analysis were evaluated.

RESULTS

Concerning alpha diversity, richness and dissimilarity differed nonsignificantly between paper point and instrument samples (P > .05), whereas a significant difference was observed in the Shannon index (P < .05). Regarding beta diversity, paper point and instrument samples presented with similar microbial community compositions (P = 1.0, PERMANOVA). Paper point controls contained significantly higher proportions of Pseudomonadales (P < .05).

CONCLUSIONS

Paper point and endodontic instrument sampling generate valid specimens for 16S rDNA community profiling. Endodontic instrument sampling is easier to execute and, therefore, could be the technique of choice.

Controlling Root Canal Infection in Oncological Patients with Apical Periodontitis

INTRODUCTION

This study evaluated the effectiveness of chemomechanical preparation associated with intracanal medication in reducing the total bacterial load of infected root canals in cancer patients undergoing antineoplastic treatment. The prevalence, levels, and response to treatment of Streptococcus and Actinobacteria species were also assessed.

METHODS

The root canals of teeth with apical periodontitis from oncological and control patients were treated using rotary instrumentation, 2.5% NaOCl irrigation, and 2-week calcium hydroxide medication (n = 23/group). Bacteriological root canal samples were taken before (S1) and after chemomechanical preparation (S2), and after intracanal medication (S3). DNA extracted from the samples was subjected to 16S rRNA gene-based quantitative real-time polymerase chain reaction assays for evaluation of the treatment effects on total bacteria, Streptococcus species, and members of the Actinobacteria phylum.

RESULTS

All S1 samples were positive for bacteria. S1-S2 and S1-S3 bacterial reduction values were highly significant (P < .01). Although bacterial counts were reduced from S2 to S3, the decrease was not statistically significant (P > .05). Intergroup comparisons showed no significant differences in S1, S2 and S3 counts (P > .05). In the oncological group, 77% of the cases were positive for bacteria in S2, and 68% in S3. In the control group, corresponding figures were 65% for both S2 and S3. There were no significant differences between groups as for streptococci and actinobacteria prevalence, levels, and response to treatment (P > .05).

CONCLUSIONS

Root canal treatment using rotary instruments, NaOCl irrigation, and calcium hydroxide medication was highly effective in reducing the bacterial populations in infected teeth with apical periodontitis from cancer patients, with no significant differences to controls.

The microbial co-infection interaction network in apical periodontitis with sinus tracts

OBJECTIVES

This study aims to characterize the bacterial co-occurrence features and potential interactions associated with the presence of sinus tracts in apical periodontitis in a Chinese population by using 16S rRNA next-generation sequencing (NGS).

METHODS

Thirty-one samples from twenty-six patients were collected from root canals. Following the extraction of the bacterial DNA, the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced. Compositional diversity, prominent taxa and co-occurrence network analysis were compared according to the presence or absence of sinus tracts.

RESULTS

The overall microbiota in two groups exhibited distinguished patterns. Actinomyces dominated in samples with sinus tracts while Prevotella was the most abundant in samples without sinus tracts. The major pathogens in sinus tracts exhibited a complex co-occurrence network, in which Pseudomonas formed a distinctive cluster with enriched abundance, and the extensive correlations centered on Desulfovibrio and Pseudoramibacter may suggest novel dependencies. In the network without sinus tracts, the Bacteroidetes and Firmicutes taxa presented close internal associations.

CONCLUSIONS

The sequencing results confirmed the complexity of the microbiota in AP. The presence of sinus tracts was associated with distinctive infective patterns and complicated microbial co-infection interaction networks. Further investigations should be adopted to elucidate the relationship between the novel interactions and disease progression.

CLINICAL SIGNIFICANCE

Exploring the microbial interactions leads to a better understanding of etiology of apical periodontitis. Utilizing next generation sequencing techniques, our research uncovered the bacterial community structure and observed co-infection networks associated with sinus tracts, providing potential insights for prognosis prediction and targeted therapeutics of persistent inflammation.

Effects of Sequential Antimicrobial Phases on Root Canal Microbiome Dynamics in Two-Visit Treatment of Primary Apical Periodontitis: A Longitudinal Experimental Study

BACKGROUND

Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication.

METHODS

Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe).

RESULTS

While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase.

CONCLUSIONS

Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments.

Microbial diversity in primary endodontic infections: demographics and radiographic characteristics

OBJECTIVE

To analyze if the microbiome community composition in primary endodontic infections is associated with clinical or radiographic factors.

MATERIALS AND METHODS

Seventy-one patients with primary endodontic infections were evaluated for percussion tenderness, presence of a sinus tract, presence of caries, sex, probing depth > 4 mm, and age. Samples from the root canals were obtained and the microbiome was subsequently characterized by 16 S rRNA amplicon sequencing. For the radiographic analysis, a subset of 12 samples with a periapical index (PAI) ≤ 2 were compared with 19 samples with PAI of 5. The Shannon and Chao1 indices were used to measure alpha diversity. Differences in abundances of genera were evaluated using the Kruskal-Wallis test with Bonferroni's correction. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bray-Curtis dissimilarity matrices.

RESULTS

No significant differences in microbiome composition relative to clinical factors were found using ANOSIM. Teeth within the two categories of periapical index showed a similar number of species richness, and alpha diversity values P > 0.05. Community composition was significantly affected by the periapical index (ANOSIM P = 0.039, R = 0.10). Larger radiographic lesions demonstrated significant increase in Prevotellaceae, Olsenella, and the motile bacteria Oribacterium, Selenomonadaceae spp., and Treponema.

CONCLUSION

Clinical factors associated with apical periodontitis have a limited impact on the root canal microbiome composition. Community composition appears to be affected in teeth with large apical lesions.

Association between endodontic symptoms and root canal microbiota: a systematic review and meta-analysis of bacteroidetes, spirochaetes and fusobacteriales

OBJECTIVES

This systematic review and meta-analysis aimed to assess the prevalence of Bacteroidetes, Spirochaetes, and Fusobacteriales in symptomatic versus asymptomatic apical periodontitis as a primary objective. The secondary objective was to evaluate the prevalence of these species independently in symptomatic and asymptomatic apical periodontitis.

MATERIALS AND METHODS

An electronic search of the PubMed, Scopus, and Open-Grey databases was carried out from November 2022 to February 2023 and was later updated through July 2024..The risk of bias was assessed using the New Castle Ottawa scale. The quality of evidence was assessed using the Grading of Recommendations. Assessment, Development, and Evaluation.

RESULTS

The initial search resulted in 968 records. Following the removal of duplicates and a review of titles and abstracts, 66 studies underwent full-texts analysis. Twenty studies were deemed eligible for inclusion. For the first outcome, a fixed-effects model was used. In a total of 7 studies with 193 participants, Spirochaetes were more prevalent in symptomatic apical periodontitis (p < .05) with a risk ratio of 1.91 [ 95% CI 1.25-2.92]. No significant difference was observed (p˃.05) in the prevalence of Bacteroidetes (12 studies with 451 participants) and Fusobacteriales (7 studies with 205 participants) in symptomatic vs asymptomatic apical periodontitis with a risk ratio of (.96), and (1.1), [95% CI, .78-1.19], and [95% CI, 0.84.1.44], respectively. The overall quality of evidence was low.

CONCLUSIONS

The confirmation of the prevalence of Bacteroidetes and Fusobacteriales in symptomatic vs asymptomatic apical periodontitis remains uncertain. However, there is an association between Spirochetes and symptomatic apical periodontitis. Additional research is required to address the limitations of the current body of evidence.

CLINICAL RELEVANCE

Identifying key pathogens in symptomatic apical periodontitis can help develop targeted interventions that address the underlying microbial causes.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

INTRODUCTION

This study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables.

METHODS

Twenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria.

RESULTS

Of 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree.

CONCLUSIONS

The bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Effects of the Irrigation Needle Design on Root Canal Disinfection and Cleaning

INTRODUCTION

This ex vivo study evaluated the disinfecting and cleaning effects of root canal preparation using sodium hypochlorite irrigation with 3 different needle designs.

METHODS

Mesial roots from extracted mandibular molars with Vertucci class II configuration were anatomically matched based on micro-computed tomography (micro-CT) analyses and distributed into 3 groups (n = 18/group). The canals were contaminated with a mixed bacterial culture for 30 days and then subjected to preparation using 2.5% sodium hypochlorite irrigation with open-ended flat needle (3 mm short of the working length - WL), closed-ended side-vented irrigation needle (1 mm short of the WL), or a closed-ended plastic needle with 2 lateral outlets (TruNatomy) (1 mm short of the WL). Bacteriological samples were taken from the canals before (S1) and after preparation (S2). After another micro-CT scan, the roots were sectioned and samples were also taken from the apical canal segment (S3). Bacterial reduction was assessed by quantitative real-time polymerase chain reaction. The amount of accumulated hard tissue debris was evaluated by micro-CT.

RESULTS

A substantial reduction in bacterial counts was observed in all 3 groups when comparing S1 with S2 (99.95%, 98.93%, and 98.90% in the open-ended, closed-ended, and TruNatomy needle groups, respectively) (P < .01). No significant differences were observed between groups for bacterial reduction in the full and apical canal (P > .05). There were no intergroup differences in the amount of accumulated hard tissue debris either (P > .05). The open-ended needle group showed significantly more specimens with quantitative real-time polymerase chain reaction negative results for bacteria in S3 than TruNatomy (P < .05).

CONCLUSION

When used up to an appropriate insertion depth, the 3 needle types result in similar antibacterial and cleaning performance, provided variables such as needle size and irrigant type, volume and flow rate are controlled. Exclusive analysis of the apical segment, including the isthmus, revealed that the open-ended needle yielded more cases negative for bacteria.

An In Vitro Evaluation of the Antimicrobial Efficacy of a Novel Irrigant Using Next-Generation Sequencing

INTRODUCTION

To evaluate the antimicrobial activity of Triton irrigation versus 4% sodium hypochlorite (NaOCl) utilizing a direct contact test and an extracted tooth model.

METHODS

In the first experiment, a direct contact test was conducted to compare bacterial DNA removal and microbial diversity changes following irrigation with 4% NaOCl or Triton. Hydroxyapatite and dentin discs were inoculated with subgingival human-derived dental plaque for 2 weeks utilizing the Center for Disease Control biofilm reactor and subsequently challenged with the root canal irrigants for 5 minutes. In the second experiment, teeth contaminated with a multispecies biofilm (n = 24) were assigned into two treatment groups, NaOCl or Triton irrigation. Samples were obtained for quantitative real-time polymerase chain reaction and next-generation sequencing analysis before and after instrumentation. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray-Curtis dissimilarity and ANOSIM was used to measure beta diversity. Differences in abundances of genera were evaluated using Kruskal-Wallis test with Bonferroni corrections.

RESULTS

The direct contact test revealed no significant differences in the bacterial load based on 16S rRNA gene molecules/μL, reads, or differences in the Shannon index among groups. In the extracted tooth model, a bacterial load reduction of log10 3.08 ± 0.69 and 2.76 ± 0.91 were found for NaOCl and Triton, respectively (P = .348). Next-generation sequencing showed fewer reads, lower Chao1, and beta diversity values when pretreatment and post-treatment samples were assessed in both experimental groups (P < .0001). The Kruskal-Wallis analysis found that 17 genera of bacteria were over-represented in minimal values in the Triton post-treatment group, 14 of these genera represented less than 1% of the microbial community.

CONCLUSIONS

Both irrigants had limited antimicrobial activity in the direct contact test. When used in conjunction with mechanical instrumentation both irrigants were able to reduce the bacterial DNA load and diversity in comparison with pretreatment communities. The NaOCl irrigation, followed by ethylenediaminetetraacetic acid flush, was more effective in decreasing DNA counts from low-abundance organisms.

Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study

AIM

To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform.

METHODOLOGY

Thirty-six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA-like differential expression tool for high-throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2.

RESULTS

The qPCR counts were significantly higher in s1 compared to s2 (p = .0007). The Chao1 index indicated no difference in alpha diversity (p < .7019); whereas Shannon (p = .0056) and Simpson (p = .02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (R2 = .0630, p = .012). Patient ID also showed a significant effect on community composition (R2 = .6961, p = .001). At the genus level, Dialister, Mogibacterium, Prevotella, and Olsenella were differentially enriched at s1, while Actinomyces, Stenotrophomonas_unclassified, Enterococcus_unclassified, and Actinomyces_unclassified were differentially enriched in s2.

CONCLUSION

The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.

Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review

BACKGROUND

Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis.

OBJECTIVES

This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis.

METHODS

The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist.

RESULTS

From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 105 to 106 in primary infections and from 103 to 104 in posttreatment infections.

DISCUSSION

Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis.

CONCLUSIONS

There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type.

REGISTRATION

PROSPERO CRD42021275886.

Effect of supplementary sodium hypochlorite agitation techniques on an ex vivo oral multispecies biofilm during passive disinfection of simulated immature roots

AIM

To compare the effect of different sodium hypochlorite (NaOCl) agitation techniques on an ex vivo oral multispecies biofilm during passive disinfection of simulated immature roots.

METHODOLOGY

Extracted human teeth were prepared to simulate immature roots. They were infected with a dental plaque-derived multispecies biofilm and cultured for 14 days. The roots were randomly designated into four groups: (1) negative control (PBS), (2) 1.5% NaOCl (CNI), (3) CNI + Ultrasonic activation (UA), (4) CNI + EasyClean agitation (ECA), (5) CNI + XP-endo finisher agitation (XPF), and (6) positive control (6% NaOCl). Biofilm samples were collected from the root canals and used to determine the number of viable cells (colony-forming units), scanning electron microscopy, and 16S rRNA gene sequencing. The mean colony-forming units per mL (CFU/mL) were analysed using One-way anova. 16S rRNA sequencing data were analysed for alpha (observed OTUs, Shannon index, and Chao1) and beta diversity (Bray-Curtis dissimilarities). The LEfSe analysis was used to determine the effect of treatment procedures on the abundance of root canal microbiota. The significance was set at .05.

RESULTS

PBS and CNI samples had significantly higher CFU/mL counts than UA, ECA, XPF, and 6% NaOCl samples (p < .05). The pre-treatment, PBS, and CNI groups had significantly greater alpha diversity than the UA, ECA, XPF, and 6% NaOCl groups (p < .05). NaOCl agitation groups and the 6% NaOCl group achieved a more pronounced reduction in bacteria from the genera Fusobacterium, Actinomyces, Porphyromonas, and Capnocytophaga.

CONCLUSIONS

The effectiveness of passive disinfection protocols was enhanced by NaOCl agitation techniques, suggesting that this supplementary method can improve the outcome of revitalization procedures.

The root canal microbiome diversity and function. A whole-metagenome shotgun analysis

AIM

To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.

METHODOLOGY

Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.

RESULTS

Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.

CONCLUSIONS

Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.

The effect of ultrasonic and multisonic irrigation on root canal microbial communities: An ex vivo study

AIM

To analyse the effect of ultrasonic irrigant activation (UIA) and the GentleWave (GW) multisonic irrigation (GW) with minimal instrumentation on the root canal microbial diversity in an ex vivo model that used extracted molars with a history of pulp necrosis.

METHODOLOGY

Twenty-three mandibular molars were prepared ex vivo for collection of superficial (surface control), pre-treatment and post-treatment samples 24 h after extraction. Samples were divided into two groups: UIA using 6% NaOCl (n = 11) and GW group (n = 12). All samples were processed using quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA next-generation sequencing to measure microbial diversity before and after the antimicrobial treatment. For qPCR, a t-test (α = .05) was used to compare the log10 reduction. The Chao1 and Shannon indices evaluated alpha diversity. Differences in community composition (beta diversity) were evaluated by analysis of similarity (ANOSIM). Kruskal-Wallis test with Bonferroni corrections was performed to evaluate the differences in abundances genera in the samples.

RESULTS

Quantitative real-time polymerase chain reaction revealed an estimated 1.6 and 2.6 log10 reduction for UIA and GW groups respectively (p = .048). An average of 5 ± 4 and 3 ± 5 operational taxonomic units (OTUs) were found in surface's samples in the UIA and GW group respectively. These values were significantly lower (p < .001) compared to the number of preoperative OTUs in those groups (155 ± 79 and 187 ± 121). In assessing beta diversity, there were no significant differences found in pre-treatment samples (R = .090, p = .070 ANOSIM with Bonferroni corrections). Also, no significant differences in community composition were observed in post-treatment samples (R = -.05, p = .829). After treatment, there was a significant reduction of Eubacterium using conventional treatment with UIA and a significant reduction of Prevotella using minimal instrumentation with GW irrigation (p = .007 and p = .002 respectively).

CONCLUSION

Quantitative PCR analysis revealed a significant reduction in microbial load for GW group. Overall, diversity changes were similar between UIA and GW irrigation in this ex vivo model that used extracted teeth with a history of pulp necrosis. OTUs obtained from the surface sample were negligible and did not affect the statistical outcome of the study.

Photodynamic therapy in the root canal treatment of primary teeth: A systematic review of clinical trials

BACKGROUND

Dental caries is the most common oral disease worldwide, and it is estimated to affect 2.3 billion people, with at least 530 million of them being schoolchildren with decayed primary teeth. This condition can rapidly evolve into irreversible pulp inflammation and pulp necrosis and thus requiring endodontic intervention. Photodynamic therapy (PDT) is a supplementary method to conventional pulpectomy and is used to improve the protocol used for disinfection.

AIM

The main objective of this study was to evaluate through a systematic review the efficacy of supplementary PDT on the pulpectomy of primary teeth. This review was registered a priori on the PROSPERO database (CRD42022310581).

DESIGN

Two independent and blinded reviewers carried out a comprehensive search in five databases: PubMed, Cochrane, Scopus, Embase, and Web of Science. Eligible studies were randomized and nonrandomized clinical trials that evaluated in vivo microbiological load or clinical outcomes after using supplementary PDT in infected primary teeth.

RESULTS

After the selection process, four studies met the inclusion criteria and were included in this study. Data regarding the sample characteristics and PDT protocols were retrieved. All included trials used phenothiazinium salts as photosensitizer agents. Only one study observed a significant difference in the in vivo microbiological load reduction outcome when performing PDT on primary teeth. The remaining studies all discussed the possible benefits of this intervention; however, none observed a significant difference in this outcome.

CONCLUSION

In this systematic review, moderate-to-low certainty of the available evidence was observed, and thus, no significant conclusions can be drawn from the findings.

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

OBJECTIVES

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.

MATERIALS AND METHODS

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.

RESULTS

Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems. 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.

CONCLUSIONS

Both treatment protocols had measurable effects on 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 aetiology of apical periodontitis were eliminated or substantially reduced.

CLINICAL RELEVANCE

The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus, and Bacteroidaceae [G-1].

Bacteriologic Conditions of the Apical Root Canal System of Teeth with and without Posttreatment Apical Periodontitis: A Correlative Multianalytical Approach

INTRODUCTION

This study used a correlative multianalytical approach to investigate the bacteriologic conditions in the apical root canal system of treated teeth with or without apical periodontitis and their correlation with the technical quality of the previous root canal obturation and the presence and volume of apical periodontitis lesions.

METHODS

Root apexes were obtained from recently extracted root canal-treated teeth with (n = 23) and without (n = 22) apical periodontitis lesions as demonstrated by cone-beam computed tomographic examination. The root apexes were sectioned and subjected to micro-computed tomographic (micro-CT) scanning. The specimens were cryopulverized, and DNA extracted from the powder was used as a template in real-time polymerase chain reaction assays to quantify total bacteria and members of the Streptococcus genus and Actinobacteria phylum. The bacteriologic findings were compared between the 2 groups and also evaluated for associations with cone-beam computed tomographic and micro-computed tomographic data.

RESULTS

Bacteria were detected in all apical canal samples except 1. The mean counts of total bacteria, streptococci, and actinobacteria did not differ significantly between teeth with or without apical periodontitis (P > .05). Streptococcus levels were significantly lower by 80% in the apical canals of teeth with small lesions compared with those without lesions (P < .05). The limit of filling >2 mm short was significantly associated with more total bacterial counts compared with canals filled 0-2 mm short (P < .05). An adequate coronal restoration was significantly associated with lesser counts of Streptococcus (P < .05).

CONCLUSIONS

Comparable bacterial loads were observed in the apical canal system of treated teeth with and without apical periodontitis, suggesting that factors other than only the total bacterial levels may also influence the development and progression of apical periodontitis. Bacteria were found in the apical canal in virtually all cases with a high prevalence of streptococci and actinobacteria. Streptococci counts were significantly higher in the apical canal of teeth with inadequate restorations and teeth with no lesions. Underfilled canals showed higher bacterial counts.

The Effectiveness of Silver Nanoparticles Mixed with Calcium Hydroxide against Candida albicans: An Ex Vivo Analysis

INTRODUCTION

The purpose of this study was to assess the antifungal activity of silver nanoparticles (AgNPs) in combination with calcium hydroxide (Ca(OH)2) against Candida albicans (C. albicans).

METHODS

AgNPs was mixed with pure Ca(OH)2 powder in an aqueous base. A standard suspension (1 × 108 bacterial cells/mL) of C. albicans was prepared in a 96-well plate and incubated on shaker at 37 °C in 100% humidity to allow fungal biofilm formation in infected dentin slices (n = 98). The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of AgNPs alone or with Ca(OH)2 were determined. The samples were separately placed in 24-well tissue culture plates and divided into three experimental groups (0.03, 0.04, and 0.06) and three control groups; negative (saline) and positive chlorhexidine gel and Ca(OH)2. Quantitative measurements of fungal activity by XTT colorimetric assay and qualitative measurements using confocal laser microscopy and scanning electron microscopy were performed.

RESULTS

The cell viability of C. albicans in the experimental groups was significantly reduced compared to the negative control group. The combination of (AgNPs (0.04%) and Ca(OH)2) was the most potent against C. albicans.

CONCLUSIONS

The findings demonstrated that combining silver nanoparticles with Ca(OH)2 was more effective against C. albicans biofilm compared to Ca(OH)2 alone, suggesting a combing effect.

Efficacy of mixed diclofenac solutions against root canal biofilms

The objective of this research was to evaluate the efficacy of diclofenac sodium solutions, with or without cetrimide (CTR) added, against polymicrobial root canal biofilms grown in dentin specimens. The study groups were: (1) 5% diclofenac sodium (DCS); (2) 2.5% DCS; (3) 2.5% DCS + 0. 2% CTR; (4) 2.5% DCS + 0.4% CTR and (5) 0.9% saline solution (SS) as the control. After 5 min of solution contact with the biofilms, the antimicrobial activity was evaluated by means of the adenosine triphosphate (ATP) assay as well as confocal laser scanning microscopy (CLSM). Microbial quantification was indicated as the percentage reduction of relative light units (RLUs) for the ATP assay, the Log10 total biovolume and the viability percentage (green cells) for CLSM. Solutions of 2.5% DCS + 0.4% CTR and 5% DCS showed the highest antimicrobial efficacy. Cetrimide increased the antibiofilm activity of diclofenac sodium against endodontic biofilms.

Bacterial diversity in primary infected root canals of a Chinese cohort: analysis of 16 S rDNA sequencing

PURPOSE

To characterize the bacterial community in the primarily infected root canals.

METHODS

A total of 13 samples were collected from the primarily infected root canals. 16 S rDNA sequencing was performed to define bacterial community. Taxonomic annotation, bacterial hierarchical structures, community richness and diversity, and inter-subject variability of the bacterial community in the root canal samples were analyzed. Gender, age, and duration of the toothache-specific bacterial community associated with the patient groups were analyzed.

RESULTS

A total of 359 Species were annotated and identified in the whole study cohort. The Alpha diversity analysis showed that the species diversity and detection rate of the 13 samples were high, which reflected the authenticity of sequencing results. The Beta diversity analysis was used to compare the degree of difference between different root canal samples. The 13 samples were divided into two groups according to the results, group A was samples I1-I12, and group B was samples I13. The bacterial species of group A samples were analyzed with the clinical characteristics of patients, and it was found that gender, and duration specific differences in bacterial species, and there was no significant difference in species types among different ages of patients.

CONCLUSION

There were a wide diversity and inter-subject variability in the bacterial community in the primary infected root canals. While Porphyromonas gingivalis was the most abundant species, Fusobacterium nucleatum was the most variable species in the bacterial community of the root canal. The bacterial community at different taxonomic levels varied from sample to sample, despite consistent disease diagnoses. There was gender, duration-specific differences in the bacterial species in the primary infected root canals.

Endodontic operative field asepsis: a comparison between general dentists and specialists

OBJECTIVE

The aim was to evaluate the establishment of an aseptic endodontic operative field in general dentistry by assessing general dentists' ability to reduce the amount of contamination to a non-cultivable level, and to compare the operative field asepsis at a general dentistry clinic with that at an endodontic specialist clinic.

MATERIALS AND METHODS

A total of 353 teeth were included in the study (153 in general dentistry, 200 at the specialist clinic). After isolation, control samples were taken, the operative fields disinfected with 30% hydrogen peroxide (1 min) followed by 5% iodine tincture or .5% chlorhexidine solution. Samples were collected from the access cavity area and buccal area, placed in a fluid thioglycolate medium, incubated (37°, 7 d), evaluated for growth/non-growth.

RESULTS

Significantly more contamination was observed at the general dentistry clinic (31.6%, 95/301), than at the endodontic specialist clinic (7.0%, 27/386) (p <.001). In general dentistry, significantly more positive samples were collected in the buccal area than in the occlusal area. Significantly more positive samples were collected when the chlorhexidine protocol had been used, both in general dentistry (p <.001) and at the specialist clinic (p =.028).

CONCLUSIONS

The result from this study shows insufficient endodontic aseptic control in general dentistry. At the specialist clinic, both disinfection protocols were able to reduce the amount of microorganisms to a non-cultivable level. The observed difference between the protocols may not reflect a true difference in the effectiveness of the antimicrobial solutions, as confounding factors may have contributed to the result.

Disinfection and Shaping of Vertucci Class II Root Canals after Preparation with Two Instrument Systems and Supplementary Ultrasonic Activation of Sodium Hypochlorite

INTRODUCTION

This study compared disinfection and shaping after root canal preparation with either XP-endo Shaper or TruNatomy instrument systems, supplemented by ultrasonic activation of sodium hypochlorite (NaOCl) with either stainless-steel (SS) or nickel-titanium (NiTi) inserts.

METHODS

Mesial roots from mandibular molars with Vertucci class II configuration were divided into 2 groups (n = 24) based on anatomically paired micro-computed tomography (micro-CT) analyses. Pre and postpreparation micro-CT scans were obtained to evaluate the shaping performance. The canals were contaminated with a mixed bacterial culture for 30 days and then subjected to preparation with either XP-endo Shaper or TruNatomy instruments using NaOCl irrigation. Supplementary ultrasonic activation of NaOCl was conducted using either an SS (TruNatomy group) or NiTi (XP-endo Shaper group) insert. Bacteriological samples were taken from the canals before preparation (S1), after preparation (S2), and after the supplementary approach (S3). Bacterial reduction was evaluated using a quantitative real-time polymerase chain reaction.

RESULTS

Preparation with both instrument systems significantly reduced bacterial counts (P < .01). After preparation, 36% (TruNatomy) and 35% (XP-endo Shaper) were negative for bacteria. These values increased to 59% and 65% after ultrasonic activation with the SS and NiTi inserts, respectively. The quantitative data in S2 showed that XP-endo Shaper promoted a significantly higher bacterial reduction than TruNatomy (P < .05). No significant intragroup differences were observed after ultrasonic activation (P > .05), probably because the SS insert promoted a significantly higher S2-to-S3 reduction than the NiTi insert (P < .01). Micro-CT analysis revealed no significant differences in the unprepared areas between the groups (P > .05).

CONCLUSIONS

The XP-endo Shaper caused a significantly higher bacterial reduction than TruNatomy in Vertucci class II canals. Better antibacterial results after ultrasonic activation were observed for the SS ultrasonic inserts than for the NiTi inserts.

What Is the Microbial Profile in Persistent Endodontic Infections? A Scoping Review

INTRODUCTION

This scoping review aimed to map the evidence about the microbiota found in persistent endodontic infections.

METHODS

The study protocol was prospectively registered and is available at https://osf.io/3g2cp. The electronic search was performed in MEDLINE via PubMed, Lilacs, BBO, Scopus, Web of Science, Cochrane Library, and Embase. The eligibility criteria were based on the PCC acronym, where P (Population) represents patients with teeth presenting persistent endodontic infection, C (Concept) represents microbial profile, and C (Context) represents undergoing endodontic retreatment. Clinical studies that evaluated the microbial profile of samples collected from root canals of teeth undergoing retreatment, using classical or molecular methods, were included. Studies that did not show a minimum period of 1 year between primary endodontic treatment and retreatment or did not radiographically evaluate the quality of primary root canal filling were excluded. Two reviewers independently selected the articles and collected data.

RESULTS

From a total of 957 articles, 161 were read in full, and 32 studies were included. The most prevalent species were Enterococcus faecalis, Parvimonas micra, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Dialister invisus, Propionibacterium acnes, Tannerella forsythia, and Treponema denticola. Cases with symptomatology or inadequate root canal filling presented an increase in specific bacterial species compared to those with no symptomatology or adequate filling. A greater number of microorganisms was observed in teeth with inadequate coronal restoration compared to those with adequate restoration.

CONCLUSIONS

Persistent endodontic infections have a polymicrobial profile identified by the commonly used methods for bacterial detection/identification and are subject to the limitations present in each of those methods.

Analysis of antimicrobial efficacy of sodium hypochlorite and ozonated water against biofilm in oval canals

This in vitro study compared the antimicrobial efficacy of 2.5% sodium hypochlorite (NaOCl) and 8 µg/mL ozonated water agitated by passive ultrasonic irrigation (PUI) or PUI combined with EndoActivator (EA) against mature multispecies biofilm. One hundred and five oval-shaped mandibular premolars were instrumented, sterilized, and inoculated with Enterococcus faecalis, Candida albicans, and Staphylococcus aureus, divided into: control group - saline; O3 group - ozonated water; O3 PUI group - ozonated water with PUI agitation; O3 PUI+EA group - ozonated water with PUI+EA agitation; NaOCl group - NaOCl; NaOCl PUI group - NaOCl with PUI agitation; and NaOCl PUI+EA group - NaOCl with PUI+EA agitation. Microbiological samples were collected before (S1) and after (S2) the disinfection procedures and the data were statistically analyzed using the Kruskal-Wallis test. In the culture method, there was significant disinfection in the O3 PUI+EA, NaOCl, NaOCl PUI, and NaOCl PUI+EA groups (p˂0.05). The combination of NaOCl with PUI+EA reduced microbial counts to zero (p˂0.05). In the qPCR method, there was a significant reduction in the total count of viable microorganisms in the O3 PUI, O3 PUI+EA, NaOCl, NaOCl PUI, and NaOCl PUI+EA groups (p˂0.05). It can be concluded that 2.5% NaOCl with and without agitation, as well as 8 µg/mL ozonated water with its action enhanced by the agitation techniques, were effective in root canal disinfection, and their antimicrobial efficacy is related to the microorganisms present in the biofilm.

Microbiome in paired root apices and periapical lesions and its association with clinical signs in persistent apical periodontitis using next-generation sequencing

AIM

To assess and compare the microbiome of paired root apices and periapical lesions from cases with failed endodontic treatment and to associate the microbiome and bacterial metabolic pathways in both sites with asymptomatic apical periodontitis (AAP) and symptomatic apical periodontitis (SAP), using next-generation sequencing (NGS).

METHODOLOGY

Matched root apices and periapical lesions of patients with failed root canal treatments were surgically extracted. Specimens were cryopulverized, bacterial DNA was extracted and the V3-V4 hypervariable regions of the 16 S rRNA gene were amplified and sequenced using the Illumina Miseq platform. Diversity and community composition were studied in the paired samples, as well as in AAP and SAP cases. Diversity indices were compared in each case by means of the Wilcoxon matched-pairs signed rank and Mann-Whitney U tests. Differences in the community composition were explored with multivariate statistical analysis and Linear discriminant analysis Effect Size (LEfSe). Bacterial functional study was performed through the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.

RESULTS

Twenty-one paired apices and lesions were successfully sequenced and analysed, identifying a total of 21 phyla and 600 genera. A higher alpha-diversity was observed in the periapical lesions, although no global differences in the community composition between the two sites were found (p = .87), the most prevalent genera being Fusobacterium, Porphyromonas and Streptococcus. Prevotella, Clostridiales_vadinBB60_group, Bosea, Phreatobacter, Afipia and Xanthobacteriaceae_unclassified were enriched in SAP samples, while Pseudopropionibacterium, Campylobacter and Peptoniphilus were significantly more abundant in AAP cases (p < .05). Metabolic pathways involved in the amino acid metabolism or degradation and flagellum assembly were more abundant in SAP samples, whereas glucose metabolism-related pathways were associated with AAP.

CONCLUSIONS

The bacterial community composition was similar in the apices and periapical lesions. The microbiome was different in AAP and SAP samples, gram-negative bacteria showing higher relative abundances in SAP cases. An association was observed between amino acid degradation and flagellum assembly pathways, and the development of tenderness to percussion or palpation.

Antimicrobial potential of new diclofenac hydrogels for disinfection in regenerative endodontics: An in vitro and ex vivo study

AIM

There is a need to explore new alternatives for root canal disinfection in regenerative endodontics, since the current strategies are far from ideal. Currently, the potential use of diclofenac (DC) is being investigated for controlling root canal infections. The objective was to evaluate the antimicrobial efficacy of novel DC-based hydrogels (DCHs) against polymicrobial biofilms grown in radicular dentine and root canals and to compare results with triantibiotic (TAH) and diantibiotic (DAH) hydrogels, and calcium hydroxide (Ca[OH]₂ ).

METHODOLOGY

The in vitro antimicrobial activity of intracanal medicaments was evaluated against 3-week-old polymicrobial root canal biofilms grown on human radicular dentine. Dentine samples were obtained and randomly divided into the study groups (n = 4/group): (1) 1 mg/ml TAH; (2) 1 mg/ml DAH; (3) 5% diclofenac (DCH); (4) 2.5% DCH; (5) 1.25% DCH; (6) 1 mg/ml DAH + 5% DCH; (7) Ca(OH)₂ paste; (8) positive control. The microbial viability, in terms of percentage of intact cell membranes, was assessed after 7 days by confocal scanning laser microscopy (CSLM). The ex vivo efficacy of intracanal medications was evaluated in root canals infected with a polymicrobial suspension. Intracanal microbiological samples at baseline (S1) and 7 days post-treatment (S2) were taken; microbial quantification and cell viability were assessed by quantitative polymerase chain reaction (qPCR) and flow cytometry (FC). The mean Log₁₀ of bacterial DNA copies in root canal samples before (S1) and the Log₁₀ reduction of DNA copies S1-S2 in qPCR were recorded. The absolute value of total cells stained, and the percentage reduction of intact membrane cells after treatment (S1-S2), were analysed by FC. Global comparison was done using the Kruskal-Wallis test, whilst the Mann-Whitney U test was used for pair-by-pair comparison.

RESULTS

Confocal scanning laser microscopy analysis indicated that the greatest effectiveness was obtained with 5% DCH, showing significant differences with respect to the other groups (p < .001). In root canals, the highest Log₁₀ DNA reduction S1-S2 was obtained with 5% DCH and TAH, with no differences between them. The results of FC showed that only 5% DCH proved significantly superior to the other treatments.

CONCLUSIONS

Sodium DC hydrogels demonstrate antimicrobial efficacy against endodontic biofilms.

Multispecies biofilm removal by a multisonic irrigation system in mandibular molars

AIM

The aim of the study was to assess biofilm removal efficacy of GentleWave System and passive ultrasonic irrigation (PUI).

METHODOLOGY

Twenty-two human mandibular molars with Vertucci's type II configuration in the mesial root were selected. Teeth were autoclaved, inoculated with dental plaque and incubated in a CDC biofilm reactor for two weeks. The mesial roots were instrumented up to 20.06 file (V-Taper) for the GentleWave group and up to 35.04 file (Vortex Blue) for PUI group. Irrigation was performed using GentleWave and PUI irrigation protocols (n = 11). Dentine debris on paper points samples were obtained for quantitative real-time polymerase chain reaction (qPCR) and 16S ribosomal RNA gene sequencing (next-generation aequencing-NGS). For qPCR, a non-parametric test (α = 0.05) was used. Next-generation sequencing data were analysed using mothur, with alpha diversity calculated as the Shannon and Chao1 indices and Bray-Curtis dissimilarities were used for beta diversity. Differences in alpha diversity and abundances of genera were evaluated using Kruskal-Wallis test. Differences in community composition were evaluated using analysis of similarity with Bonferroni correction for multiple comparisons.

RESULTS

Quantitative real-time polymerase chain reaction results showed that the reduction estimated in percentages for both groups was equivalent (p > .05). NGS analysis showed that both techniques promoted a significant reduction in reads and OTUs number (p < .05). Shannon alpha diversity and Chao1 index showed no differences between pre- or post-treatment samples for both groups (p > .05). Additionally, pre-treatment communities differed from post-treatment samples in both groups regarding bacterial taxa reduction (ANOSIM R = 0.50 and 0.55, p < .001).

CONCLUSIONS

Bacterial reduction in mesial roots of mandibular molars prepared to 35.04 with PUI was similar to those prepared to 20.06 with a multisonic irrigant activation system.

Microbiome Changes During Regenerative Endodontic Treatment Using Different Methods of Disinfection

INTRODUCTION

The purpose of this study was to characterize qualitatively and quantitatively the changes in the endodontic microbiome, in teeth with necrotic pulp, open apexes and apical periodontitis, with three antimicrobial protocols, undertaken in a multicenter clinical trial.

METHODS

Microbiological samples were collected from 116 RET teeth, and 97 qualified for inclusion. The teeth were randomly divided into three treatment groups: apexification (APEX), regeneration (REGEN) and revascularization (REVASC), all in two appointments. The group variables in the first appointment irrigants, and second appointment irrigants and medicaments were as follows: APEX: 5.25-6% NaOCl, 5.25-6% NaOCl + 17% EDTA and calcium hydroxide; REGEN: 1.25% NaOCl, 17% EDTA and 0.1 mg/mL triple antibiotic paste (TAP); and REVASC 5.25% NaOCl, saline and 1g/mL TAP, respectively. Sampling was done upon access (S0), after irrigation in the first appointment (S1), and after using medication and irrigation in the second appointment (S2).

RESULTS

Quantitative PCR analysis of the 16S rRNA gene showed significant reduction in bacterial load from S0 to S2 in all groups; however, the APEX and REVASC groups had significantly less residual DNA than the REGEN group (p=0.0045). The relative abundance of Bacteroidetes, Fusobacteria, Spirochaetes and Synergistetes were reduced with the treatment rendered. However, relative abundance of Firmicutes and Actinobacteria was not changed, and that of Proteobacteria increased. LEfSe analysis showed that reduction in bacterial taxa was more in REVASC than APEX which in turn was more than in REGEN.

CONCLUSION

Enhanced antimicrobial protocols lead to better reduction in quantitative and qualitative parameters of the endodontic microflora.

Enhancing the intracanal antibacterial effects of sodium hypochlorite with etidronic acid or citric acid

INTRODUCTION

This study evaluated the bacterial reduction promoted by root canal preparation using irrigation with sodium hypochlorite (NaOCl) alone, associated with etidronic acid (HEDP) or alternated with citric acid, and after a supplementary agitation step.

METHODS

Extracted mandibular premolars were selected and distributed into 3 groups based on anatomically paired micro-computed tomographic analyses. The canals were contaminated with Enterococcus faecalis for 30 days and then subjected to chemomechanical preparation with a reciprocating instrument under irrigation with NaOCl alone, mixed with HEDP (NaOCl/HEDP), or alternated with citric acid (NaOCl/CA). A supplementary agitation step with the XP-endo Finisher was performed in all groups. Intracanal bacteriological samples were taken before (S1) and after preparation (S2), and after the supplementary approach (S3). DNA was extracted from the samples and subjected to quantitative real-time polymerase chain reaction.

RESULTS

Intragroup analyses revealed a substantial bacterial reduction from S1 to S2 or S3 in all groups (p<0.01). The supplementary agitation resulted in S2-to-S3 bacterial reduction of 6%, 68%, and 80% in the NaOCl, NaOCl/HEDP, and NaOCl/CA groups, respectively. Irrigation with NaOCl alone resulted in 53% and 47% of samples negative for bacteria in S2 and S3, respectively. Corresponding figures for NaOCl/HEDP were 75% and 85%, and 44% and 72% for NaOCl/CA. Intergroup analyses of S2 samples showed that NaOCl/HEDP was significantly more effective than the other two in reducing the bacterial levels (p<0.05). After the supplementary approach, both NaOCl/HEDP and NaOCl/CA were significantly more effective than NaOCl alone (p<0.05), with no significant differences between them (p>0.05).

CONCLUSION

Both the freshly combined NaOCl/HEDP solution and the alternate use of NaOCl and citric acid followed by XP-endo Finisher agitation resulted in significantly higher intracanal bacterial reduction than NaOCl alone.

The Novel Role of Solvents in Non-Surgical Endodontic Retreatment

Non-surgical endodontic retreatment is a reliable conservative option for managing post-treatment apical periodontitis. However, effective microbial control, based on the maximization of filling removal and disinfection protocols, is not yet predictable. Traditional gutta-percha solvents, which are indistinctively used for both the core and sealer filling materials, became obsolete due to unprecedented advances in endodontic technology. Nonetheless, microtomography, scanning electronic microscopy findings, and histobacteriological analysis tend to confirm the persistence of filling materials and the lack of association between root canal enlargement and superior disinfection. There is a controversy regarding the most suitable clinical protocols surrounding the shaping procedures and the supplementary disinfection steps. Based on the literature and the previous work of the team, the authors aimed to summarize the current knowledge regarding specific solvent formulations that target filling materials. Additionally, the advantage of an additional irrigation step to optimize disinfection was highlighted. This adjunctive procedure serves a dual role in the dissolution of filling materials, and in conferring an antibiofilm effect. Further research is needed to understand the novel contribution of these strategies upon clinical practice outcomes.

Present Status and Future Directions - Canal Shaping

This narrative review will focus on the evolution, present and future of engine‐driven root canal preparation. Root canal preparation changed drastically when Walia in 1988 introduced the use of nickel‐titanium (NiTi) alloys in Endodontics. In 2013, five generations of NiTi endodontic instruments had been established based on their metallurgical, mechanical properties and design features. Since then, manufacturers have been introducing further major changes in instrument design and characteristics that have not been translated in new recognized generations of instruments. In general, those changes have demonstrated enhanced instrument properties, but it is not clear yet if all those improvements are directly translated to an improvement in clinical success. This narrative review attempts to address the present status of engine‐driven instruments in terms of both evidence from laboratory‐based studies and clinical data, to identify potential further generations of instruments, and last to anticipate future directions for research and development.

Present status and future directions - microbiology of endodontic infections

Apical periodontitis has a microbial aetiology and is one of the most common inflammatory diseases that affect humans. Fungi, archaea and viruses have been found in association with apical periodontitis, but bacteria are by far the most prevalent and dominant microorganisms in endodontic infections. Bacterial infection of the root canal system only occurs when the pulp is necrotic or was removed for previous treatment. In some specific cases, including acute and chronic abscesses, the bacterial infection may reach the periradicular tissues. Intracanal bacteria are usually observed as sessile multispecies communities (biofilms) attached to the dentinal root canal walls. Infection in the main root canal lumen can spread to other areas of the root canal system. Although more than 500 bacterial species have been detected in endodontic infections, a selected group of 20 to 30 species are most frequently detected and may be considered as the core microbiome. There is a high interindividual variability in the endodontic microbiome in terms of species composition and relative abundance. Obligate anaerobic species are more abundant in the intraradicular bacterial communities of teeth with primary apical periodontitis, while both anaerobes and facultatives dominate the communities in post-treatment apical periodontitis. Bacterial interactions play an essential role in determining the overall virulence of the community, which has been regarded as the unit of pathogenicity of apical periodontitis. This article reviews the microbiologic aspects of endodontic infections and provides perspectives for future research and directions in the field.