Microbiome in the Apical Root Canal System of Teeth with Post-Treatment Apical Periodontitis

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.

Exploring the root canal microbiome in previously treated teeth: A comparative study of diversity and metabolic pathways across two geographical locations

AIM

To analyse and compare the root canal microbiome present in root-filled teeth of two different geographical populations, and to study their functional potential using a next-generation sequencing approach.

METHODOLOGY

Sequencing data obtained from surgical specimens from previously treated teeth with periapical bone loss from Spain and USA were included in the study. Taxa were classified using SILVA v.138 database. Differences in genera abundances among the 10 most abundant genera were evaluated using a Kruskal-Wallis test. Alpha diversity indices were calculated in mothur. The Shannon and Chao1 indices were used. Analyses of similarity (ANOSIM) to determine differences in community composition were done in mothur, with Bonferroni correction for multiple comparisons. p-Values < .05 were considered statistically significant. Identification of enriched bacteria function prediction in the study groups (KEGG pathways) was carried out by linear discriminant analysis effect size (LEfSe) via Python 3.7.6.

RESULTS

A greater alpha-diversity (Shannon and Chao1 indices) was observed from samples obtained in Spain (p = .002). Geography showed no significant effects on community composition via an ANOSIM using Bray-Curtis dissimilarities (R = 0.03, p = .21). Bacterial functional analysis prediction obtained by PICRUSt showed that 5.7% KEGG pathways differed between the Spain and US samples.

CONCLUSIONS

The taxonomic assessment alone does not fully capture the microbiome's differences from two different geographical locations. Carbohydrate and amino acid metabolism were enriched in samples from Spain, while samples from USA had a higher representation of pathways related to nitrogen, propanoate metabolism, and secretion systems.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research

AIM

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis.

METHODOLOGY

Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant.

RESULTS

Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4.

CONCLUSIONS

The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

The effect of the enzymes trypsin and DNase I on the antimicrobial efficiency of root canal irrigation solutions

The purpose of this study was to evaluate the antibacterial efficacy of using 2.5% NaOCl, 2% chlorhexidine (CHX), Irritrol, and chitosan-coated silver nanoparticles (AgCNPs) alone or in combination with deoxyribonuclease I (DNase I) and trypsin pre-enzyme applications in dentin samples contaminated with Enterococcus faecalis (E. faecalis) by CLSM. 144 dentin blocks with confirmed E. faecalis biofilm formation were divided randomly according to the irrigation protocol (n = 12): NaOCl, CHX, Irritrol, AgCNPs, trypsin before NaOCl, CHX, Irritrol, AgCNPs, and DNase I before NaOCl, CHX, Irritrol, AgCNPs. Dentin blocks were stained with the Live/Dead BacLight Bacterial Viability Kit and viewed with CLSM after irrigation applications. The percentage of dead and viable bacteria was calculated using ImageJ software on CLSM images. At a significance level of p < 0.05, the obtained data were analyzed using one-way Anova and post-hoc Tukey tests. In comparison with NaOCl, CHX had a higher percentage of dead bacteria, both when no pre-enzyme was applied and when DNase I was applied as a pre-enzyme (p < 0.05). There was no difference in the percentage of dead bacteria between the irrigation solutions when trypsin was applied as a pre-enzyme (p > 0.05). AgCNPs showed a higher percentage of dead bacteria when trypsin was applied as a pre-enzyme compared to other irrigation solutions (p < 0.05), while the pre-enzyme application did not affect the percentage of dead bacteria in NaOCl, CHX, and Irritrol (p > 0.05). No irrigation protocol tested was able to eliminate the E. faecalis biofilm. While the application of trypsin as a pre-enzyme improved the antimicrobial effect of AgCNPs, it did not make any difference over other irrigation solutions.

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.

High-performing cross-dataset machine learning reveals robust microbiota alteration in secondary apical periodontitis

Multiple research groups have consistently underscored the intricate interplay between the microbiome and apical periodontitis. However, the presence of variability in experimental design and quantitative assessment have added a layer of complexity, making it challenging to comprehensively assess the relationship. Through an unbiased methodological refinement analysis, we re-analyzed 4 microbiota studies including 120 apical samples from infected teeth (with/without root canal treatment), healthy teeth, using meta-analysis and machine learning. With high-performing machine-learning models, we discover disease signatures of related species and enriched metabolic pathways, expanded understanding of apical periodontitis with potential therapeutic implications. Our approach employs uniform computational tools across datasets to leverage statistical power and define a reproducible signal potentially linked to the development of secondary apical periodontitis (SAP).

The effect of root canal preparation tapers on planktonic bacteria and biofilm reduction in the apical third: A correlative microtomography and microbiological laboratory study

AIM

To evaluate the influence of different preparation tapers on the reduction in planktonic bacteria and biofilms of Enterococcus faecalis and Candida albicans in the apical third (4 mm) of the mesial roots of mandibular molars, correlating decontamination with canal shape.

METHODOLOGY

After microtomography analysis for morphological standardization of the canals, 48 mandibular molar roots, each containing two canals (96 canals), were contaminated with E. faecalis and C. albicans and divided into four groups (n = 11) for canal instrumentation using ProDesign Logic 2 files with different tapers G (.03): # 25.03; G (.04): # 25.04; G (.05): # 25.05; and G (.06): # 25.06 and irrigation with 2.5% sodium hypochlorite. Four roots were examined under a scanning electron microscope (SEM) to qualitatively assess biofilm formation. Eight roots were used as the negative control group (samples were not contaminated). Bacteriological samples were taken exclusively from the apical third of the roots before and after chemical-mechanical preparation and bacterial counts were determined (CFU/mL). The final micro-CT scan was used to quantify the volume variation and unprepared canal area in the apical third. Statistical analysis was performed using the Kruskal-Wallis, Student-Newman-Keuls and Wilcoxon tests for analysis of microbiological data. anova and the Tukey or Games-Howell test were used for analysis of micro-CT data and Spearman's test for correlations (α = 5%).

RESULTS

All groups showed a significant reduction in bacteria (p < .05), with no statistically significant difference between groups. There was no significant difference in per cent volume increase between groups. The unprepared area (Δ%) was affected by the file used (p = .026) and was significantly lower for G (.06) compared to G (.03). There was no statistically significant correlation among bacterial reduction, volume and unprepared area (p > .05).

CONCLUSION

The different preparation tapers influenced root canal shaping in the apical third but did not improve decontamination in this region.

Microbiota Association and Profiling of Gingival Sulci and Root Canals of Teeth with Primary or Secondary/Persistent Endodontic Infections

INTRODUCTION

Microbiota associated with primary endodontic infection (PEI) and secondary/persistent endodontic infection (SPEI) must be characterized to elucidate pathogenesis in apical periodontitis and bacterial biomarkers identified for diagnostic and therapeutic applications.

METHODS

This study analyzed the microbial community profiles of root canals and gingival sulci (sulcus-E) for teeth with PEI (n = 10) or SPEI (n = 10), using the Illumina MiSeq platform. Bacterial samples from gingival sulci (sulcus-C) of healthy contralateral teeth served as controls.

RESULTS

There were 15 phyla, 177 genera, and 340 species identified. The number and diversity of bacteria in root canals did not differ significantly between PEI and SPEI. Proteobacteria, Firmicutes, Fusobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in both groups. At the genus level, Lancefieldella, Bifidobacterium, Stomatobaculum, and Schaalia were enriched in root canals with SPEI. Of significance, Lancefieldella was observed in both root canals and sulcus-E of teeth with SPEI. At the species level, Neisseria macacae, Streptococcus gordonii, Bifidobacterium dentium, Stomatobaculum longum, and Schaalia odontolytica were increased significantly in root canals with SPEI compared to PEI. Oribacterium species, Streptococcus salivarius, Lancefieldella parvula, Prevotella denticola, and Oribacterium asaccharolyticum were more abundant in sulcus-E of teeth with SPEI compared to PEI.

CONCLUSIONS

There were distinctive and differing predominant bacterial species associated with the root canals and gingival sulci between teeth with PEI and SPEI. Specific bacteria identified in sulcus-E and root canals of teeth with SPEI could serve as noninvasive diagnostic biomarkers for detecting SPEI.

Microbiological assessment of success and failure in pulp revitalization: a randomized clinical trial using calcium hydroxide and chlorhexidine gluconate in traumatized immature necrotic teeth

Aim

To compare differences in the disinfection efficacy of calcium hydroxide (CH) and chlorhexidine gluconate (CHD) dressings in pulp revitalization (PR) of traumatized immature necrotic teeth; to investigate the microflora in successful/failed PR and whether bacterial persistence influences the outcomes of PR.

Methods

Microbiological assessment of the average bacterial load (CFU/sample) and bacterial diversity (taxa/sample) was performed on 41 teeth at three timepoints (S2-before, S3-after debridement and S5- after root canal dressing).

Results

The primary microflora was more diverse in successful cases than in failed. Decreases in CFU/sample and taxa/sample occurred S2 - S3, though new increases occurred at S5 in the CHD subgroup (successful and failed) and CFU/sample in the CH subgroup (failed). At S5, the successful cases showed more bacterial decreases. No specific species was associated with the outcomes with no statistical differences between the disinfection efficacy.

Conclusions

There were no statistical differences in CH and CHD efficacy. At S5, microflora persisted in both successful and failed outcomes, but the abundance and diversity increased significantly only in the failed cases. The successful outcomes presented higher diversity and higher decreases of the primary microflora at S5 than the failed outcomes. The abundance and diversity increased significantly at S5 only in failed cases.

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.

CLSM-Guided Imaging for Quantifying Endodontic Disinfection

Elimination of microbes in the root canal system is crucial for achieving long-term success in endodontic treatment. Further efforts in study design and standardization are needed in order to improve the validity and comparability of in vitro results on endodontic disinfection procedures, in turn improving clinical outcomes. This study optimizes two models at all steps: tooth selection, pretreatment, inoculation method (by growth or centrifugation), and confocal laser scanning microscopy (CLSM)-guided imaging of LIVE/DEAD-stained specimens. Individual anatomical conditions lead to substantial differences in penetration depth. Sclerosis grading (SCG), a classification system introduced in this study, provides information about the sclerosis status of the dentine and is helpful for careful, specific, and comparable tooth selection in in vitro studies. Sonically activated EDTA for the pretreatment of roots, inoculation of Enterococcus faecalis in an overflow model, 3-4 weeks of incubation, as well as polishing of dentine slices before staining, led to advances in the visualization of bacterial penetration and irrigation depths. In contrast, NaOCl pretreatment negatively affected performance reproducibility and should be avoided in any pretreatment. Nonsclerotized teeth (SCG0) can be used for microbial semilunar-shaped inoculation by centrifugation as a "quick-and-dirty" model for initial orientation. In conclusion, CLSM-guided imaging for quantifying endodontic infection/disinfection is a very powerful method after the fine-tuning of materials and methods.

Profiling Antibiotic Susceptibility among Distinct Enterococcus faecalis Isolates from Dental Root Canals

Enterococcus faecalis, a leading multi-resistant nosocomial pathogen, is also the most frequently retrieved species from persistently infected dental root canals, suggesting that the oral cavity is a possible reservoir for resistant strains. However, antimicrobial susceptibility testing (AST) for oral enterococci remains scarce. Here, we examined the AST profiles of 37 E. faecalis strains, including thirty-four endodontic isolates, two vanA-type vancomycin-resistant isolates, and the reference strain ATCC-29212. Using Etest gradient strips and established EUCAST standards, we determined minimum inhibitory concentrations (MICs) for amoxicillin, vancomycin, clindamycin, tigecycline, linezolid, and daptomycin. Results revealed that most endodontic isolates were susceptible to amoxicillin and vancomycin, with varying levels of intrinsic resistance to clindamycin. Isolates exceeding the clindamycin MIC of the ATCC-29212 strain were further tested against last-resort antibiotics, with 7/27 exhibiting MICs matching the susceptibility breakpoint for tigecycline, and 1/27 reaching that of linezolid. Both vanA isolates confirmed vancomycin resistance and demonstrated resistance to tigecycline. In conclusion, while most endodontic isolates remained susceptible to first-line antibiotics, several displayed marked intrinsic clindamycin resistance, and MICs matched tigecycline's breakpoint. The discovery of tigecycline resistance in vanA isolates highlights the propensity of clinical clone clusters to acquire multidrug resistance. Our results emphasize the importance of implementing AST strategies in dental practices for continued resistance surveillance.

Prevalence of Fusobacterium Species in Endodontic Infections Detected With Molecular Methods: Systematic Review and Meta-Analysis

INTRODUCTION

Endodontic infections are polymicrobial; however, investigating the role of bacterial species is critical because they may influence pathogenesis, the development of symptoms, or the persistence of disease. This systematic review aimed to determine the prevalence of Fusobacterium species and its association with different types of endodontic infections.

METHODS

MEDLINE (Ovid), PubMed, Scopus, Web of Science, and Cochrane Library databases were used as electronic databases to retrieve relevant studies. The studies were evaluated for eligibility criteria, and the certainty in evidence and risk of bias were evaluated using critical appraisal tools for prevalence studies from the Joanna Briggs Institute. Forty studies were selected for meta-analysis and statistically analyzed for the relationship between the prevalence of Fusobacterium species and both the presence of symptoms and the type of infections (primary vs secondary/persistent) using meta-regression analysis.

RESULTS

The prevalence of Fusobacterium spp. in endodontic infections ranged from 3%-100% (mean = 42.51%) in the 40 included studies. Calculated confidence intervals indicated that the presence of Fusobacterium spp. was not statistically associated with the presence of symptoms or with the type of infections (the set of 2 predictors was not significant; P < .05).

CONCLUSIONS

The prevalence of Fusobacterium infection, which was identified with molecular methods, was not significant for overall regression using both predictors (ie, symptoms [symptomatic vs asymptomatic] and types of infections [primary vs secondary/persistent]).

The presence of Enterococcus faecalis in saliva as a risk factor for endodontic infection

Aim

The aim of the present study was to investigate and correlate the prevalence of Enterococcus faecalis in saliva and in root canals with different pulpal and periapical conditions.

Methodology

Sixty-seven patients were divided into five groups based on pulpal and periapical tissue status: healthy vital teeth (HVT, n=7), healthy treated teeth without lesion (HTT, n=9), irreversible pulpitis (IP, n=13), necrosis (N, n=18), and post-treatment apical periodontitis (PTAP, n=20). Saliva, rubber dam, sterility control and pre-treatment root canal samples were collected and microbiologically processed by culture method. The phylogenetic relationship of E. faecalis isolates collected from root canals and saliva were investigated by whole genome sequencing. Fisher’s exact test was used to correlate the presence of E. faecalis in root canals or saliva with clinical and/or radiographic findings. Linear/logistic regression analyses were performed to establish the relationship between the presence of E. faecalis in root canals, saliva, and the status of periapical tissues.

Results

E. faecalis was found in 18 root canal and saliva samples. E. faecalis root canal isolates were recovered with the highest frequency from post-treatment apical periodontitis. The occurrence of E. faecalis in saliva was strongly associated with its detection in the root canals (P &lt; 0.001). The pretreatment presence of E. faecalis in root canals was associated with significantly higher odds of having periapical lesions (OR=11.03; 95% CI, 1.27-95.70; p &lt; 0.05). Saliva and root canal isolates from the same patient were highly correlated at the phylogenetic level (Jaccard index &gt;0.95).

Conclusion

This pilot study confirms the role of E. faecalis in developing peri-radicular lesions in secondary endodontic infections and suggests that saliva could be the main source of infection. Further studies are needed to investigate the exact origin of this bacteria and its true role in the pathogenesis of secondary/persistent endodontic infections.

Microbiological profile of root canals indicated for endodontic retreatment due to secondary endodontic infections or for prosthetic reasons

OBJECTIVE

The objective of this study was to evaluate the microbiological profile of root canals indicated for endodontic retreatment due to secondary endodontic infections evidenced by the presence of chronic apical periodontitis (G1) or for prosthetic reasons, without clinical and radiographic signs of endodontic reinfection (G2).

METHODS

Microbiological samples were collected from thirty teeth (N=30) out of which 15 were indicated for retreatment due to the presence of chronic apical periodontitis (G1) and 15 were indicated exclusively for prosthetic reasons (G2). Samples were collected from root canals before (S1), after chemomechanical preparation (S2), and after 30 days of intracanal medication composed of calcium hydroxide and 2% chlorhexidine gel (S3). The molecular analysis was performed using Nested-PCR for the detection of 17 bacterial species. The efficacy of each stage of the retreatment in reducing the microbial load was verified by counting colony-forming units (CFU). The statistical analysis considered a significance level of 5%.

RESULTS

The results showed that bacteria were detected in 100% of the cases in S1, in both groups, by Nested PCR. The most frequently found species in S1 in both groups were Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Parvimonas micra. The microbial load of G1 was higher than G2 in the initial samples (S1). Endodontic retreatment was effective in reducing the microbial load in G1 and G2. Statistically significant associations were found between specific bacteria and clinical signs and symptoms.

CONCLUSION

It was concluded that the microbial community present in the root canal of teeth indicated for endodontic retreatment is mixed and heterogeneous. G1 and G2 differ in the number of species per case and microbial load.

CLINICAL RELEVANCE

Endodontic retreatment was effective in reducing the microbial load. Statistically significant associations were found between specific bacteria and clinical signs and symptoms.

Taxonomic abundance in primary and secondary root canal infections

AIM

To evaluate the root canal microbiome composition in cases of primary and secondary apical periodontitis.

METHODOLOGY

Thirty-nine samples from patients with primary root canal infections obtained before root canal treatment, and 40 samples obtained during root-end resection procedures from previously filled cases with apical periodontitis were evaluated using 16S rRNA next-generation sequencing analysis (NGS). Demographic and clinical factors included age, sex, infection type, percussion sensitivity, and presence of pain. Differences in abundances of genera were evaluated using Kruskal-Wallis test. Alpha and beta diversity indices were calculated using mothur. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray-Curtis dissimilarity was used to measure beta diversity. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bonferroni correction for multiple comparisons.

RESULTS

Significantly fewer operational taxonomic units values were observed from samples from secondary infections (p < .0001). While no significant differences were observed in the Chao 1 index between primary and secondary infections, the Shannon alpha diversity was significantly lower in secondary relative to primary infections (p = .008). Among samples, sex, age (adult vs. older adult), percussion sensitivity, and presence of pain all showed no significant effects on community composition via an analysis of similarity (ANOSIM). However, community composition was significantly different depending on whether the sample was from a primary or secondary infection (R = .051, p = .03). Nine microbial genera comprised the predominant taxa observed among samples (>3.3%) and included Parvimonas, Fusobacterium, Campylobacter, Arachnia, Eubacterium, Prevotella, Peptostreptococcus, Fretibacterirum, and Pseudoramibacter. Significantly greater relative abundances of Prevotella, Peptostreptococcus, Veillonella, Lactucaseibacillus, and Dialister were observed in primary infections.

CONCLUSIONS

Primary endodontic infections are more diverse than secondary infections. The microbial composition is not associated with the clinical manifestations of apical periodontitis.

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.

Comparison of conventional and contemporary root canal disinfection protocols against bacteria, lipoteichoic acid (LTA), and lipopolysaccharide (LPS)

This study devised a dual-species biofilm model to investigate bacteria, lipoteichoic acid (LTA), and lipopolysaccharide (LPS) simultaneously, and compared the efficacy of conventional and contemporary disinfection protocols. Seventy single-rooted mandibular premolars were included. Fourteen teeth were negative control, and 56 teeth were infected with 3-week-old E. faecalis and E. coli GFP biofilm. Fourteen/56 teeth were positive control, with seven teeth processed for CLSM analysis and seven teeth sampled with paper points (PPs) and cryogenically ground for bacterial, LTA, and LPS analyses. Forty-two teeth were randomly divided into three groups: GWS (GentleWave system) + MIT (minimally invasive technique), PUI (passive ultrasonic irrigation) + CIT (conventional instrumentation technique), and XP-EF (XP-endo Finisher) + CIT (All, n = 14). Samples were collected before (s1) and after disinfection (s2) with PPs and after cryogenically ground (s3). CFUs were counted, and LTA and LPS were quantified with LTA-ELISA and LAL assay, respectively. XP-EF was as effective as PUI (p > 0.05). GWS + MIT was the most effective disinfection protocol against bacteria, LTA, and LPS (p < 0.05). In conclusion, PUI, XP-EF, and GWS were highly effective against bacteria, LTA, and LPS, with GWS being the most effective.

A simplified method for detecting Gram-positive and Gram-negative bacteria in dental histological samples: A preliminary and comparative study

OBJECTIVE

Bacteria identification inside the dental tissue is a complex procedure requiring specific protocols. This study aimed to compare two classical Gram staining methods with a new staining method proposed by the authors to detect Gram-positive and Gram-negative bacteria in dental histological samples of human dentin.

METHODS

Ten human teeth, extracted because of various pathologies, were decalcified, dehydrated, and paraffin-embedded. Then, approximately 100 serial sections of 4 µm thickness were made per sample. The serial sections were placed on glass slides and were stained according to Brown-Brenn, Brown-Hopps, and a proposed modification of Brown-Brenn staining. Both ATCC strains, smeared on glass slides, were stained following each method's instructions used in histological samples.

RESULTS

From a qualitative evaluation, the Brown-Brenn method resulted in better staining of Gram-positive bacteria, while the authors' proposed staining technique was more oriented towards Gram-negative bacteria. On the other hand, the Brown-Hopps showed quite a balance in detecting Gram-positive and Gram-negative bacteria. Unlike the Brown-Brenn stain, the other two protocols showed better stainability of Gram-negative microorganisms in bacterial-smeared samples.

CONCLUSION

All staining techniques evaluated in this article can identify bacteria, but the outcome can change according to the staining procedure used.

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.

The 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 one-year CBCT-based outcomes of molar root canal treatment were improved through an Enhanced infection protocol (EnP), when compared to 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 enhanced infection control protocol 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 either treatment under EnP or StP. To compare the differential effect of the protocol on the identity of bacteria present, one hundred and fifty, 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, prior to 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 two treatment groups.

RESULTS

88 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 to 38.3 in the StP. Reduced diversity and richness measures were noted in the EnP pre-obturation samples compared to the StP in OTU, Chao1 and ACE indices (p≤0.05). 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 enhanced infection control protocol 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.

Impact of dentin conditioning and sealer modification with chitosan-hydroxyapatite nanocomplexes on the antibacterial and mechanical characteristics of root dentin

INTRODUCTION

This study aimed to characterize the effectiveness of dentin-conditioning with bio-mineralizable chitosan-hydroxyapatite precursor (CS-HA) nanocomplexes alone or associated with tricalcium silicate sealer (TCS/CS-HA) on the mechanical property and antibiofilm efficacy in root dentin.

METHODS

Flow tests were performed following ISO6876:2012-specifications. Solubility was measured. Micromorphology was assessed using Scanning Electron Microscopy (SEM). Nanohardness/elastic modulus were also determined. Fracture resistance was determined on lower premolars that were prepared, and randomly distributed among 7-groups (n=8/group), including the control, CS-HA dentin-conditioning and root canal filled groups. Similar canal preparation/distribution procedure was followed to test the antibacterial effect on Enterococcus faecalis-infected roots. Descriptive statistic was used to report SEM findings. Flowability results were analyzed using Paired t-test. Multiple comparisons from solubility, fracture and antibacterial assays were assessed by one-way ANOVA-Tukey's tests.

RESULTS

TCS/CS-HA showed optimal flow and no effect on solubility after immersion for 4 weeks (p>.05). TCS/CS-HA significantly increased nanohardness and elastic modulus (210±11.3MPa, 7.9±0.9GPa) compared to TCS (44.5±7.8MPa, 2.1±0.3GPa,p<.05). SEM revealed needle-shaped mineralized structures resulting in fewer voids and a well-adapted sealer-dentin interface in the TCS/CS-HA groups. NaOCl-EDTA irrigation resulted in reduced fracture resistance (444.34N) while CS-HA dentin-conditioning alone (928.28N, p<.05) and CS-HA dentin-conditioning plus CS-HA/TCS resulted in higher fracture resistance (1134.06N, p<.05). CS-HA dentin-conditioning also reduced bacteria by 2.04 log (4.50±0.43) from the initial bacterial load (6.54±0.07, p<.05). There was further bacterial reduction when CS-HA-conditioned root canals were filled with TCS or TCS/CS-HA (0.00 to 0.98±0.57, p>.05).

CONCLUSION

Dentin modification with CS-HA increased the fracture resistance of root dentin, and decreased the residual bacterial burden. TCS/CS-HA potentiated the nanomechanical and physical properties of TCS.

Present status and future directions - irrigants and irrigation methods

Irrigation is considered the primary means of cleaning and disinfection of the root canal system. The purpose of this review was to set the framework for the obstacles that irrigation needs to overcome, to critically appraise currently used irrigants and irrigation methods, to highlight knowledge gaps and methodological limitations in the available studies and to provide directions for future developments. Organization of bacteria in biofilms located in anatomic intricacies of the root canal system and the difficulty to eliminate them is the main challenge for irrigants. Sodium hypochlorite remains the primary irrigant of choice, but it needs to be supplemented by a chelator. Delivery of the irrigants using a syringe and needle and activation by an ultrasonic file are the most popular irrigation methods. There is no evidence that any adjunct irrigation method, including ultrasonic activation, can improve the long‐term outcome of root canal treatment beyond what can be achieved by instrumentation and syringe irrigation. It is necessary to redefine the research priorities in this field and investigate in greater depth the penetration of the irrigants, their effect on the biofilm and the long‐term treatment outcome. New studies must also focus on clinically relevant comparisons, avoid methodological flaws and have sufficiently large sample sizes to reach reliable conclusions. Future multidisciplinary efforts combining the knowledge from basic sciences such as Chemistry, Microbiology and Fluid Dynamics may lead to more effective antimicrobials and improved activation methods to bring them closer to the residual biofilm in the root canal system.

Comparison of GentleWave system and passive ultrasonic irrigation with minimally invasive and conventional instrumentation against LPS in infected root canals

This study compared the effectiveness of GentleWave system (GWS) and passive ultrasonic irrigation (PUI) in removing lipopolysaccharides (LPS) from infected root canals after minimally invasive (MIT) and conventional instrumentation (CIT) techniques. Sixty first premolars with two roots were inoculated with fluorescent LPS conjugate (Alexa Fluor 594). Of those, twelve were dentin pretreated, inoculated with fluorescent LPS conjugate, and submitted to confocal laser scanning microscopy (CLSM) to validate the LPS-infection model. Forty-eight teeth were randomly divided into treatment groups: GWS + MIT, GWS + CIT, PUI + MIT, and PUI + CIT (all, n = 12). Teeth were instrumented with Vortex Blue rotary file size 15/0.04 for MIT and 35/0.04 for CIT. Samples were collected before (s1) and after a root canal procedure (s2) and after cryogenically ground the teeth (s3) for intraradicular LPS analysis. LPS were quantified with LAL assay (KQCL test). GWS + MIT and GWS + CIT were the most effective protocols against LPS, with no difference between them (p > 0.05). PUI + CIT was more effective than PUI + MIT (p < 0.05) but less effective than GWS + MIT and GWS + CIT. GWS was the most effective protocol against LPS in infected root canals using MIT and CIT techniques.

Evaluation of the effectiveness of GentleWave System and passive ultrasonic irrigation with minimally invasive and conventional instrumentation technique against Enterococcus faecalis lipoteichoic acid (LTA) in infected root canals

INTRODUCTION

This study evaluated the effectiveness GentleWave System (GWS) and passive ultrasonic irrigation (PUI) in removing E. faecalis lipoteichoic acid (LTA) from infected root canals with minimally invasive (MIT) and conventional instrumentation techniques (CIT).

METHODS

Sixty extracted human maxillary first premolars were included. All teeth were dentin pretreated and inoculated with LTA prepared from Enterococcus faecalis. First, twelve teeth were cryogenically ground to investigate the viability of recovering intraradicular E. faecalis LTA. After, forty-eight teeth were randomly divided into groups: GWS + MIT, GWS + CIT, PUI + MIT, and GWS + CIT (all =12). Teeth were instrumented with Vortex Blue rotary file size 15/.04 for MIT and 35/.04 for CIT. Samples were collected before (s1) and after a root canal procedure (s2) with sterile/ apyrogenic paper points and after cryogenically ground for intraradicular LTA analysis (s3). LTA was quantified with the LTA ELISA kit.

RESULTS

E. faecalis LTA was recovered from 100% of the samples (48/48) at s1. GWS + MIT and GWS + CIT were the most effective protocols against E. faecalis LTA, with no difference between them (p>.05). PUI + CIT was more effective than PUI + MIT (p<.05) but less effective than GWS + MIT and GWS + CIT (p<.05). GWS groups showed more root canals with undetected E. faecalis LTA after treatment than all groups tested.

CONCLUSIONS

GWS + MIT and GWS + CIT were the most effective protocol against E. faecalis LTA in infected root canals.

Improving the microbial sampling and analysis of secondary infected root canals by passive ultrasonic irrigation

OBJECTIVE

The persistence of pathogenic microorganisms in root canals is the most common reason for the failure of root canal treatment and the necessity of a root filling treatment, which results in an uncertain prognosis due to technical complexity and the variety of highly adaptable microorganisms. This study evaluated the effect of passive ultrasonic irrigation (PUI) on the outcome of the microbial analysis of root canal-treated teeth with persistent or recurrent apical inflammation in vivo.

MATERIALS AND METHODS

Sample collection was performed after root filling removal (sample S1, control group) and after PUI with NaCl (sample S2) using sterile paper points. In total, 19 samples were obtained. Quantification was performed by means of serial dilution of the samples. Subcultivated pure cultures were identified using MALDI-TOF MS complemented by the Vitek-2-System or PCR, followed by sequencing of the 16S rRNA gene. The results of the samples (S1 and S2) were evaluated regarding their bacterial count and composition.

RESULTS

The total count of bacteria and the number of aerobic/facultative anaerobic microorganisms significantly increased in the S2-samples after application of PUI. The number of obligate anaerobic microorganisms showed an increase after PUI, although it was not significant. We detected 12 different aerobic/facultative anaerobic microorganisms before PUI, and in 21 cases after PUI. Two different obligate anaerobic microorganisms were found in S1 samples compared to nine different species in S2 samples.

CONCLUSIONS

PUI is a powerful method for detaching bacteria in infected root canals and enables a more precise analysis of the etiology of persistent endodontic infections.

CLINICAL RELEVANCE

This study indicates that PUI exerts a positive cleansing effect and adds to the accessibility of microorganisms during the application of bactericidal rinsing solution in root canal treatments.

A critical analysis of research methods and experimental models to study irrigants and irrigation systems

Irrigation plays an essential role in root canal treatment. The purpose of this narrative review was to critically appraise the experimental methods and models used to study irrigants and irrigation systems and to provide directions for future research. Studies on the antimicrobial effect of irrigants should use mature multispecies biofilms grown on dentine or inside root canals and should combine at least two complementary evaluation methods. Dissolution of pulp tissue remnants should be examined in the presence of dentine and, preferably, inside human root canals. Micro-omputed tomography is currently the method of choice for the assessment of accumulated dentine debris and their removal. A combination of experiments in transparent root canals and numerical modeling is needed to address irrigant penetration. Finally, models to evaluate irrigant extrusion through the apical foramen should simulate the periapical tissues and provide quantitative data on the amount of extruded irrigant. Mimicking the in vivo conditions as close as possible and standardization of the specimens and experimental protocols are universal requirements irrespective of the surrogate endpoint studied. Obsolete and unrealistic models must be abandoned in favour of more appropriate and valid ones that have more direct application and translation to clinical Endodontics.

Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges

The oral cavity is the habitat of several hundreds of microbial taxa that have evolved to coexist in multispecies communities in this unique ecosystem. By contrast, the internal tissue of the tooth, i.e., the dental pulp, is a physiologically sterile connective tissue in which any microbial invasion is a pathological sign. It results in inflammation of the pulp tissue and eventually to pulp death and spread of inflammation/infection to the periradicular tissues. Over the past few decades, substantial emphasis has been placed on understanding the pathobiology of root canal infections, including the microbial composition, biofilm biology and host responses to infections. To develop clinically effective treatment regimens as well as preventive therapies, such extensive understanding is necessary. Rather surprisingly, despite the definitive realization that root canal infections are biofilm mediated, clinical strategies have been focused more on preparing canals to radiographically impeccable levels, while much is left desired on the debridement of these complex root canal systems. Hence, solely focusing on "canal shaping" largely misses the point of endodontic treatment as the current understanding of the microbial aetiopathogenesis of apical periodontitis calls for the emphasis to be placed on "canal cleaning" and chemo-mechanical disinfection. In this review, we dissect in great detail, the current knowledge on the root canal microbiome, both in terms of its composition and functional characteristics. We also describe the challenges in root canal disinfection and the novel strategies that attempt to address this challenge. Finally, we provide some critical pointers for areas of future research, which will serve as an important area for consideration in Frontiers in Oral Health.

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.

Infective endocarditis and oral health-a Narrative Review

Infective endocarditis is a rare but usually severe and often fatal inflammatory disease affecting the endocardial surface, native and prosthetic valves or cardiac devices. Besides various staphylococcus species, oral viridans streptococci are known to play a crucial role in the development of endocarditis, especially in patients with underlying cardiac conditions, such as valve replacement, congenital heart disease and a history of previous infective endocarditis. Particularly undetected persisting odontogenic infections and their secondary symptoms, as well as various therapeutic measures for their prevention and treatment, may lead to bacterial transfer from the oral cavity into the bloodstream, eventually enabling bacterial adherence to endocardial surfaces and thus promoting infective endocarditis. The administration of antibiotics prior to dental interventions in order to prevent this mechanism was initially recommended almost seventy years ago and has been the subject of research and intensive discussion ever since. Recently, numerous professional societies worldwide have published guidelines and updates on the prevention of endocarditis with divergent recommendations regarding the requirement of prophylactic antibiotic regimen prior to dental procedures. The objective of this article was therefore to review the currently available literature regarding oral health and infective endocarditis and to examine the rationale behind the inconsistent recommendation situation, critically.

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

Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.

The antibacterial effect and the incidence of post-operative pain after the application of nano-based intracanal medications during endodontic retreatment: a randomized controlled clinical trial

OBJECTIVE

This clinical trial aimed to evaluate the effect of nano-silver and nano-calcium hydroxide intracanal medicaments (ICM) during retreatment regarding their antibacterial effect and their effect on post-operative pain and flare-ups.

MATERIALS AND METHODS

Sixty-nine patients scheduled for endodontic retreatment were included in this randomized clinical trial and randomly allocated to 3 equal groups (n = 23) according to the type of ICM used. The first microbial sampling (S1) representing the original microbiota was obtained after the removal of the old canal filling. After chemo-mechanical debridement, another sample (S2) was obtained representing the microbial state before ICM application. Patients were randomly allocated to receive either nano-silver (nano-Ag), nano-calcium hydroxide (nano-CH), or calcium hydroxide (CH) as ICM. Patients rated their pain pre-operatively and then after 6, 12, 24, 48, and 72 h. During the second visit (7 days later), the last microbial sample (S3) was obtained after removal of the ICM. Reduction of total bacterial and total E. faecalis counts and the biofilm-forming capability of the existing microbiota were determined.

RESULTS

Results showed reduction in total bacterial count, total E. faecalis count and the biofilm-forming,capability of the existing microbiota after chemo-mechanical debridement (S1-S2) and after the application of ICM (S3-S2). However, the reduction after cleaning and shaping was significantly more pronounced (p < 0.001) compared to the effect of ICM application, with no difference between the 3 ICM (p > 0.05). Post-operative pain was significantly reduced at the 48- and 72-h intervals after the application of nano-Ag and nano-CH only (p < 0.001), with no significant difference between these two ICM (p > 0.05). The incidence of flare-ups in all groups was similar (p > 0.05).

CONCLUSIONS

The antibacterial effect of the nano-Ag and nano-CH was equivalent to that of CH, but they contributed to better pain control.

CLINICAL RELEVANCE

Nanoparticles may have a positive impact on post-endodontic pain.

Model system parameters influence the sodium hypochlorite susceptibility of endodontic biofilms

AIM

To evaluate in a laboratory setting the influence of several model system parameters on the sodium hypochlorite (NaOCl) susceptibility of endodontic biofilms. Based on these findings, a relevant in vitro endodontic biofilm model is proposed.

METHODOLOGY

In vitro biofilms were cultured, varying the following experimental model parameters: biofilm composition (monospecies Enterococcus faecalis and a multispecies biofilm including E. faecalis, Fusobacterium nucleatum, Prevotella intermedia and Porphyromonas gingivalis), incubation time (24 h or 11 days), incubation atmosphere (aerobically or anaerobically) and biofilm substrate (polystyrene microtiter plate wells, hydroxyapatite or dentine). Biofilms were subjected to treatment with NaOCl (0.025%, 0.1%, 0.5%, 2.5%) for 1 min, control groups included treatment with purified water. Biofilms were harvested and the number of surviving cells was determined by plate counting using general (monospecies biofilms) or selective (multispecies biofilms) media. A two-way ANOVA was used to explore the effect of the model parameters on biofilm eradication. Finally, the most physiologically relevant biofilm model (11-day-old multispecies biofilm grown anaerobically on dentine discs) was characterized by selective media plate counting, NaOCl susceptibility testing, scanning and transmission electron microscopy.

RESULTS

There was no difference in NaOCl eradication between the anaerobically and aerobically grown E. faecalis biofilms. One-day-old biofilms of E. faecalis were more susceptible to most tested NaOCl concentrations than 11-day-old biofilms (p < .05). When grown in a multispecies biofilm, E. faecalis was significantly less susceptible to NaOCl treatment than in a monospecies biofilm (p < .05). E. faecalis in a multispecies biofilm grown in a MTP was more susceptible to NaOCl (0.025% and 0.1%) than when grown on hydroxyapatite or dentine. No difference in biofilm NaOCl susceptibility was seen between hydroxyapatite and dentine. The multispecies biofilm proved to be a reproducible model with high NaOCl resistance, complex structure and organization.

CONCLUSION

The parameters biofilm age, biofilm composition and substrate had a significant influence on the NaOCl susceptibility of E. faecalis biofilms. Older biofilms, multispecies biofilms and biofilms grown on dentine and hydroxyapatite had reduced NaOCl susceptibility. These findings emphasize the importance of selecting relevant parameters when designing a laboratory biofilm model system for the evaluation of antimicrobial treatments.

Antibacterial Effect of Endodontic Disinfections on Enterococcus Faecalis in Dental Root Canals-An In-Vitro Model Study

Enterococcus faecalis (E. faecalis) is rather unsusceptible to many root canal disinfections which often cause a therapeutic problem. Therefore, the present in vitro study observed the efficiency of different endodontic antiseptics in their capability to suppress E. faecalis, especially inside dentinal tubules. Prior to any testing, root canals of extracted third human molars were inoculated with E. faecalis for 48 h. Antiseptic dressings with chloramine-T or calcium hydroxide (CaOH) for 24 h or irrigations with 1.3% sodium hypochlorite (NaOCl) were applied with n = 10 in each group. As control irrigation with normal saline was used. All treated canals were manually enlarged from size ISO 50 to 110 and the ablated dentin debris was subjected to microbial culture analysis. Bacterial colonization of the dentinal tubules up to 300 µm was verified by scanning electron microscopy and histological sample preparation. Application of crystalline chloramine-T caused total bacterial suppression inside the dentinal tubules. Dressings with CaOH showed only minor effects. Irrigation with NaOCl caused total eradication of bacteria adhering to the root canal walls, but also failed to completely suppress E. faecalis inside the dentinal tubules. The study showed that chloramine-T is of strong antiseptic activity and also efficient in suppressing E. faecalis inside dentinal tubules.

Molecular characterization and antibacterial activity of oral antibiotics and copper nanoparticles against endodontic pathogens commonly related to health care-associated infections

OBJECTIVE

To carry out molecular characterization and determine the antibacterial activity of oral antibiotics and copper nanoparticles (Cu-NPs) against endodontic strains isolated from persistent infections.

MATERIALS AND METHODS

Root canal samples from 24 teeth in different patients with persistent endodontic infections were obtained. The isolated strains were identified by biochemical tests and 16S rDNA sequencing. Genotyping was achieved by molecular methods. The antibacterial activity of antibiotics and copper nanostructures was determined by using minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values. Furthermore, a time-kill kinetics assay was evaluated. Nonparametric tests (Kruskal-Wallis ANOVA) were performed (p value <0.05).

RESULTS

Twenty-one isolated strains were identified. Six isolates of Enterococcus faecalis were grouped into two clusters of three isolates each, two of which were clones. All were clarithromycin-resistant and erythromycin. Eight Pseudomonas putida presented two clusters, two Pseudomonas spp. were not clonal, and all were resistant to the tested antibiotics except tetracycline. Two of five strains of Cutibacterium acnes were clonal, and all were resistant only to metronidazole. The lowest MIC and MBC values were obtained with Cu-NPs. Time-kill kinetics using Cu-NPs showed a significant decrease in all tested species within 4 h and reached 100% in 2 h for C. acnes.

CONCLUSION

In this study, in relation to health care-associated infections, endodontic strains of each species isolated at least in one patient were polyclonal. In Pseudomonas spp., at least one clone was shared between patients. E. faecalis and C. acnes strains were susceptible to low Cu-NP concentrations, while Pseudomonas spp. strains were resistant.

CLINICAL RELEVANCE

Assessing and keeping track of the susceptibility of clinical strains to antimicrobial compounds is important for the clinical outcome. Based on our results, Cu-NPs could be an alternative for endodontic treatment, in order to avoid selection of resistant strains.

Antimicrobial Efficacy of Silver Nanoparticles as Root Canal Irrigant's: A Systematic Review

Removal of microbes is imperative during endodontic therapy. Due to their antimicrobial property, silver nanoparticles have been used for endodontic irrigation of the root canals. The objective of the present study was to provide a qualitative analysis of the published literature assessing silver nanoparticles as root canal irrigants. A search of PubMed, SCOPUS, Web of Science, and Embase databases was done without any time restriction. Articles published in English were included. Data were extracted and the risk of bias was assessed. Of the 154 studies identified, after screening according to the inclusion criteria, five in vitro studies were included. The results indicate that silver nanoparticles have an anti-microbial effect to varying degrees depending on certain factors. Within the limitations of the present studies that have a moderate to low risk of bias, an antimicrobial effect of silver nanoparticles is observed. Silver nanoparticles have the potential to be used as endodontic irrigants, although their efficacy depends on particle size and the duration of contact which require further investigation.

Can Probiotics Emerge as Effective Therapeutic Agents in Apical Periodontitis? A Review

Apical periodontitis (AP) is a biofilm-associated disease initiated by the invasion of dental pulp by microorganisms from the oral cavity. Eradication of intracanal microbial infection is an important goal of endodontic treatment, and this is typically accomplished by mechanical instrumentation and application of sodium hypochlorite and chlorhexidine. However, these agents are tissue-irritating at higher concentrations and cytotoxic. Certain probiotics have been found effective in controlling marginal periodontitis, as evidenced by reduction of pathogenic bacterial loads, gains in clinical attachment levels, and reduced bleeding on probing. In vitro studies have shown inhibitory activity of some probiotics against endodontic pathogens. Similarly, in vivo studies in rats have demonstrated a positive immuno-modulatory role of probiotics in AP, as manifested by decreased levels of proinflammatory markers and increased levels of anti-inflammatory markers. A role for probiotics in effecting a reduction of bone resorption has also been reported. This review provides an outline of current research into the probiotic management of AP, with a focus on understanding the mechanisms of their direct antagonistic activity against target pathogens and of their beneficial modulation of the immune system.

Quantification of Bacterial Colonization in Dental Hard Tissues Using Optimized Molecular Biological Methods

Bacterial infections of root canals and the surrounding dental hard tissue are still a challenge due to biofilm formation as well as the complex root canal anatomy. However, current methods for analyzing biofilm formation, bacterial colonization of root canals and dental hard tissue [e.g., scanning electron microscopy, confocal laser scanning microscopy (CLSM) or determination of colony forming units (CFU)] are time-consuming and only offer a selective qualitative or semi-quantitative analysis. The aim of the present study is the establishment of optimized molecular biological methods for DNA-isolation and quantification of bacterial colonization via quantitative PCR (qPCR) from dental hard tissue. Root canals of human premolars were colonized with Enterococcus faecalis. For isolation of DNA, teeth were then grinded with a cryo mill. Since the hard tissues dentin and especially enamel belong to the hardest materials in the human organism, the isolation of bacterial DNA from root dentin is very challenging. Therefore, treatment steps for the isolation of DNA from grinded teeth were systematically analyzed to allow improved recovery of bacterial DNA from dental hard tissues. Starting with the disintegration of the peptidoglycan-layer of bacterial cells, different lysozyme solutions were tested for efficacy. Furthermore, incubation times and concentrations of chelating agents such as EDTA were optimized. These solutions are crucial for the disintegration of teeth and hence improve the accessibility of bacterial DNA. The final step was the determination of prior bacterial colonization of each root canal as determined by qPCR and comparing the results to alternative methods such as CFU. As a result of this study, optimized procedures for bacterial DNA-isolation from teeth were established, which result in an increased recovery rate of bacterial DNA. This method allows a non-selective and straightforward procedure to quantify bacterial colonization from dental hard tissue. It can be easily adapted for other study types such as microbiome studies and for comparable tissues like bones.

The benefit of culture-independent methods to detect bacteria and fungi in re-infected root filled teeth: a pilot study

AIM

To identify dominant microorganisms in root filled teeth with apical periodontitis by Pan-PCRs in comparison with a culture-dependent approach, focusing on fungal species profiling.

METHODOLOGY

The root filling material (gutta-percha) removed from 42 teeth with periapical radiolucencies undergoing root canal retreatments was analysed by molecular genetics techniques. Real-Time Pan-PCRs were conducted for the diagnosis of predominant bacteria (targeting 16S rDNA) and fungi (targeting ITS1-2 region). Identification of microorganisms was performed by Sanger sequencing of the PCR products and BLAST analysis. Additionally, subgingival plaque samples were collected and cultured to review the composition of the microbial flora. The McNemar test and the repeated measures anova were used for statistical analyses (significance level was set at P < 0.05).

RESULTS

Overall, 42/42 plaque samples had bacterial growth, whereas 32/42 gutta-percha samples had bacterial growth with a dominance of Streptococcus spp. (12/42) and Enterococcus faecalis (9/42). The mean number of bacterial taxa per gutta-percha sample was 1.6 cultivatable taxa, significantly lower than in the plaque sample that had six taxa/sample (P < 0.001). Fungus-specific cultures were negative for gutta-percha samples, and only one plaque sample had growth of a fungus. In total, 36/42 plaque samples were positive in bacterial Pan-PCRs. In bacterial Pan-PCRs of 31/42 gutta-percha samples, dominant microorganisms were identified including Streptococcus spp. (5/42) and E. faecalis (4/42). Moreover, in 7/42 gutta-percha samples, DNA of bacteria which are difficult-to-cultivate in microbiology routine culture (Acinetobacter,Pyramidobacter,Bacteroidetes,Synergistes,Atopobium and Pseudoramibacter) was found. DNA of Candida spp. was detected in 5/42 root canals by fungal Pan-PCR (1/5) and genus-specific Candida-PCR (5/5).

CONCLUSIONS

Pan-PCR assays remain appropriate as a broad-range approach for the detection of a dominant pathogen in gutta-percha samples which have less diverse microbial composition. The molecular genetic Pan-PCR approach has the advantage of detecting microorganisms that are as-yet-uncultivable or difficult-to-cultivate and should be therefore complement conventional microbiological diagnostics.

Antimicrobial effect of photodynamic therapy on intracanal biofilm: A systematic review of in vitro studies

BACKGROUND

Antimicrobial photodynamic therapy (A-PDT), is one of the adjunctive therapies developed to improve the effectiveness of root canal disinfection.. The aim of this study was to analyze the antimicrobial effect of PDT on intracanal biofilm.

METHODS

Two reviewers conducted a literature search in PubMed, MEDLINE, Lilacs, SciELO, EMBASE and Google Scholar using the following search strategy: photochemotherapy "[Mesh] OR (photodynamic therapy) AND" dental plaque "[Mesh] OR (dental biofilm) AND (root canal). The following data were collected: publication year, author's name, study site, type of study, participant number, type of photosensitizer, type of laser, method of data collection, application time and results. Study quality was assessed using the Methodological Index for Non-Randomized Studies (MINORS).

RESULTS

After selection based on title, abstract and full text, 27 studies were included in this systematic review. PDT reduced bacterial viability in most studies when combined with conventional endodontic techniques.

CONCLUSION

PDT reduced bacterial counts in most studies, especially when used as an adjunct to the conventional endodontic technique to treat refractory infection. However, PDT effects on in vitro bacterial biofilm were not accurately quantified because of the numerous biases in the studies reviewed.

Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment

OBJECTIVE

To characterize the microbiota of teeth with endodontic treatment failure by 16S ribosomal RNA genetic sequencing (GS) and PCR at the different phases of the endodontic retreatment and to associate the presence of specific bacteria with clinical and radiographic features in teeth with apical periodontitis.

MATERIALS AND METHODS

Twenty infected root canals of single-rooted teeth were selected. Samples were collected with sterile paper points before chemo-mechanical preparation (CMP) (S1), after CMP (S2) and after 30 days of intracanal medication (ICM) (S3). Microbial identification was performed using GS and PCR. Tukey-Kramer post hoc test and post hoc ANOVA were used for intergroup analysis. Paired t test and repeated-measures ANOVA were applied for intragroup analysis, at a significance level of 5%.

RESULTS

A total of 89 strains were identified using GS. Sixty-five strains were recovered in S1 and 15 strains in S2, and 9 strains remained in S3. Enterococcus faecalis was the most predominant bacteria. Gram-positive cocci bacteria predominated. Gram-negative species were also detected. Using species-specific PCR primers to detect seven species, the most prevalent ones at all the phases of the endodontic retreatment were E. faecalis and Porphyromonas gingivalis. However, Parvimonas micra and P. gingivalis were associated with previous pain, P. gingivalis was associated with tenderness to percussion and E. faecalis, Fusobacterium nucleatum and P. gingivalis were associated with periapical lesion > 3 mm.

CONCLUSIONS

In conclusion, the microbiota of persistent infection is polymicrobial with predominance of E. faecalis and P. gingivalis in all phases of the endodontic retreatment, regardless of the method used for microbial identification. Associations were found between specific bacteria and clinical/radiographic features.

CLINICAL RELEVANCE

The characterization of the bacteria present at all phases of the endodontic retreatment is important for the monitoring of the effectiveness of the techniques used and to better understand the susceptibility of these species to the disinfection agent used during the procedures.

A Pilot Study of Chronological Microbiota Changes in a Rat Apical Periodontitis Model

Apical periodontitis caused by microbial infection in the dental pulp is characterized by inflammation, destruction of the pulpal and periradicular tissues, and alveolar bone resorption. We analyzed the chronological changes in microbiota using a pyrosequencing-based approach combined with radiologic and histopathologic changes in a rat apical periodontitis model. During the three-week observation, the pulp and periapical area showed a typical progress of apical periodontitis. A total of 27 phyla, 645 genera, and 1276 species were identified. The root apex had a lower bacterial species diversity than the pulp chamber. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were dominant phyla in both the pulp chamber and root apex. Remarkably, bacterial communities showed a tendency to change in the root apex based on the disease progression. At the genus level, Escherichia, Streptococcus, Lactobacillus, Rodentibacter, and Bacteroidetes were dominant genera in the pulp chamber. The most abundant genera in the root apex were Bradyrhizobium, Halomonas, and Escherichia. The species Azospirillum oryzae increased in the pulp chamber, whereas the species Bradyrhizobium japonicum and Halomonas stevensii were highly observed in the root apex as the disease progressed. The experimental rat model of apical periodontitis demonstrated a relationship between the microbiota and the apical periodontitis progression.

Cone-beam Computed Tomographic and Micro-computed Tomographic Evaluations of the Root Apexes of Teeth with Posttreatment Apical Periodontitis

INTRODUCTION

This study evaluated the association of different variables that may influence the outcome of root canal treatment through cone-beam computed tomographic (CBCT) and micro-computed tomography (micro-CT) assessments of root apexes obtained by endodontic microsurgery of teeth with posttreatment apical periodontitis (AP), the agreement between CBCT and micro-CT findings, and the association of these variables with symptoms or lesion size.

METHODS

Clinical and CBCT records and root apexes obtained by endodontic microsurgery from 11 cases of symptomatic AP and 22 cases of asymptomatic AP were available. Apical root specimens were further scanned using micro-CT imaging. CBCT parameters included periapical radiolucency size, apical extent/density of root canal filling, and occurrence of procedural errors. Micro-CT images evaluated the same parameters plus the presence of filling material in lateral canals and ramifications, the volume of the filled/nonfilled apical root canal, and the percentage of the nonfilled canal space. The agreement between CBCT/micro-CT observations was evaluated.

RESULTS

Mandibular teeth, a lesion size <5 mm, a nonfilled volume <0.04 mm³, and the decreased percentage of the nonfilled canal volume were significantly associated with symptomatic AP. Maxillary teeth and inadequate apical filling density were significantly associated with larger lesions. Agreement between CBCT/micro-CT scores varied from fair (procedural errors) to satisfactory (extent/density of filling).

CONCLUSIONS

Tooth location, lesion size, the nonfilled apical canal volume, and the percentage of the nonfilled apical canal volume were associated with symptomatic AP. In addition, lesion size was significantly associated with tooth location and apical root canal filling density. CBCT imaging may not provide a reliable evaluation of procedural errors associated with posttreatment disease.

The apical root canal system microbial communities determined by next-generation sequencing

The aim of this study was to explore the microbial communities of endodontic infections at their apical portion by 16S rRNA Illumina sequencing and delineate the core microbiome of root canal infections and that of their associated clinical symptomatology. Samples were collected from fifteen subjects presenting one tooth with a root canal infection, and their associated symptoms were recorded. Samples were collected from the apical third of roots using a #10 K file and then amplified using multiple displacement amplification and PCR-amplified with universal primers. Amplicons were sequenced (V3–V4 hypervariable region of the 16S rRNA gene) using MiSeq (Illumina, CA). The microbial composition of the samples was determined using QIIME and HOMINGS. Data were analyzed using t tests and ANOVA. A total of 1,038,656 good quality sequences were obtained, and OTUs were assigned to 10 bacterial phyla, led by Bacteroidetes (51.2%) and Firmicutes (27.1%), and 94 genera were represented primarily by Prevotella (17.9%) and Bacteroidaceae G-1 (14.3%). Symptomatic teeth were associated with higher levels of Porphyromonas (p < 0.05) and Prevotella. P. endodontalis and P. oris were present in both cores. The present study demonstrated the complexity of the root canal microbiome and the “common denominators” of root canal infections and identified taxa whose virulence properties should be further explored. The polymicrobial etiology of endodontic infections has long been established. However, few studies have focused on expanding the breadth and depth of coverage of microbiome-infected root canals at their apical portion.

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.