Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing

Microbial composition and diversity in intraradicular biofilm formed in situ: New concepts based on next-generation sequencing

This study aimed to characterize the taxonomic composition of intraradicular multispecies biofilms (IMBs) formed in situ in a model to reproduce clinical conditions. Twelve palatal roots of maxillary molars had its canals prepared. Two roots were randomly selected to sterility control. Ten intraoral prosthetic appliances with lateral slots were fabricated. The roots were positioned in the slots with the canal access open to the oral cavity. Eight volunteers wore the appliance for 21 days, and two wore it at two different time points. One root from each appliance was removed and stored at -20°C until DNA extraction and sequencing (n = 10). Biofilm was analyzed using next-generation sequencing and bioinformatics. The V4 hyper-variable region of the 16SrRNA gene was amplified and sequenced. For data analyses, the mothur pipeline was used for 16SrRNA processing, and subsequent analyses of the sequence dataset were performed in R using the MicrobiomeAnalyst R package. The taxonomy-based analysis of bacterial communities identified 562 operational taxonomic units (OTUs), which belonged to 93 genera, 44 families, and 8 phyla. Bacterial colonization was different for each biofilm, and samples did not have the same group of bacteria. Alpha and beta diversity analysis revealed some general patterns of sample clustering. A core microbiome of prevalent OTUs and genera was identified. IMBs were heterogeneous when analyzed individually, but some diversity patterns were found after sample clustering. The experimental model seemed to reproduce the actual biofilm composition in endodontic infections, which suggests that it may be used to evaluate disinfection protocols.

Microbial composition and diversity in intraradicular biofilm formed in situ: New concepts based on next-generation sequencing

This study aimed to characterize the taxonomic composition of intraradicular multispecies biofilms (IMB) formed in situ in a model to reproduce clinical conditions. Twelve palatal roots of maxillary molars had its canals prepared. Two roots were randomly selected to sterility control. Ten intraoral prosthetic appliances with lateral slots were fabricated. The roots were positioned in the slots with the canal access open to the oral cavity. Eight volunteers wore the appliance for 21 days, and two wore it at two different time points. One root from each appliance was removed and stored at -20°C until DNA extraction and sequencing (n = 10). Biofilm was analyzed using next-generation sequencing and bioinformatics. The V4 hyper-variable region of the 16SrRNA gene was amplified and sequenced. For data analyses, the mothur pipeline was used for 16SrRNA processing, and subsequent analyses of the sequence dataset were performed in R using the Microbiome Analyst R package. The taxonomy-based analysis of bacterial communities identified 562 operational taxonomic units (OTUs), which belonged to 93 genera, 44 families, and 8 phyla. Bacterial colonization was different for each biofilm, and samples did not have the same group of bacteria. Alpha and beta diversity analysis revealed some general patterns of sample clustering. A core microbiome of prevalent OTUs and genera was identified. IMBs were heterogeneous when analyzed individually, but some diversity patterns were found after sample clustering. The experimental model seemed to reproduce the actual biofilm composition in endodontic infections, which suggests that it may be used to evaluate disinfection protocols.

Relationship of MMP-9 with the clinical course of apical periodontitis and the main bacterial species in the oral microbiota

Bacterial products, host immune cells and cytokines have been reported to play an important role in the pathogenesis of apical periodontitis (AP). This study aimed to determine the main bacterial species in the microbiota as gram positive and negative and to compare the relationship between matrix metalloproteinase (MMP)-9 and tumor necrosis factor (TNF)-α with controlled patient groups. 60 patients with AP and extraction indication were included in the study. 30 systemically healthy volunteers without AP were selected as the control group. After access cavity preparation, an initial microbiologic sample (S1) was taken from the root canal. After atraumatic extraction of the tooth, a second microbial sample (S2) was taken from the extraradicular region. After bacterial DNA extraction, 16S rRNA gene primer was designed for sequence analysis. Bacterial community profiling was made by Sanger sequencing of the PCR products. In addition, serum MMP-9 and TNF-α levels were measured from all patients. TNF-α levels of the AP group were higher than the control group, while MMP-9 levels were found to be lower (p = 0.0264 and p = 0.0146, respectively). There was no difference in the main bacterial species isolated from the samples taken from the intracanal and extraradicular region of the tooth with AP (p = 0.714). The main bacterial species in the intracanal region of the tooth with AP are similar to the main bacterial species in the extraradicular region. The pathophysiology of the tooth with AP is associated with low MMP-9 and high TNF-α, independent of the bacterial species in the intracanal and extraradicular regions.

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.

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 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.

Understanding painful versus non-painful dental pain in female and male patients: A transcriptomic analysis of human biopsies

Dental pain from apical periodontitis is an infection induced-orofacial pain condition that presents with diversity in pain phenotypes among patients. While 60% of patients with a full-blown disease present with the hallmark symptom of mechanical allodynia, nearly 40% of patients experience no pain. Furthermore, a sexual dichotomy exists, with females exhibiting lower mechanical thresholds under basal and diseased states. Finally, the prevalence of post-treatment pain refractory to commonly used analgesics ranges from 7-19% (∼2 million patients), which warrants a thorough investigation of the cellular changes occurring in different patient cohorts. We, therefore, conducted a transcriptomic assessment of periapical biopsies (peripheral diseased tissue) from patients with persistent apical periodontitis. Surgical biopsies from symptomatic male (SM), asymptomatic male (AM), symptomatic female (SF), and asymptomatic female (AF) patients were collected and processed for bulk RNA sequencing. Using strict selection criteria, our study found several unique differentially regulated genes (DEGs) between symptomatic and asymptomatic patients, as well as novel candidate genes between sexes within the same pain group. Specifically, we found the role of cells of the innate and adaptive immune system in mediating nociception in symptomatic patients and the role of genes involved in tissue homeostasis in potentially inhibiting nociception in asymptomatic patients. Furthermore, sex-related differences appear to be tightly regulated by macrophage activity, its secretome, and/or migration. Collectively, we present, for the first time, a comprehensive assessment of peripherally diseased human tissue after a microbial insult and shed important insights into the regulation of the trigeminal system in female and male patients.

Real-time optical detection of endodontic infection using bacterial autofluorescence

OBJECTIVES

For successful root canal treatment (RCT), it is essential to objectively assess the presence and activity of bacteria in the root canal system. However, current methods rely on subjective observations of root canal exudates. This study aimed to confirm whether real-time optical detection using bacterial autofluorescence can evaluate endodontic infection status by assessing the red fluorescence (RF) detected from root canal exudates.

METHODS

During RCT, endodontic paper points were used to collect root canal exudates scored using conventional organoleptic tests to assess the severity of root canal infections. RF on the paper points was assessed using quantitative light-induced fluorescence (QLF) technology. RF intensity and area from the paper points were quantified, and their correlations with infection severity were assessed using their organoleptic scores. The oral microbiome composition of RF samples was compared with non-red fluorescent (non-RF) samples.

RESULTS

The RF detection rate was nil and >98% in the non-infectious and severe groups. The RF intensity and area significantly increased with infection severity (p<0.001) and showed strong correlations with organoleptic scores (r=0.72, 0.82, respectively). The diagnostic accuracy for detecting root canal infection using RF intensity was good to excellent (AUC = 0.81-0.95) and increased with infection severity. The microbial diversity of the RF samples was significantly lower than that of the non-RF samples. Gram-negative anaerobic bacteria such as Prevotella and Porphyromonas were more predominant in RF samples.

CONCLUSIONS

Optical detection using bacterial autofluorescence can objectively evaluate endodontic infection status in real-time by assessing the RF of endodontic root canal exudates.

CLINICAL SIGNIFICANCE

This real-time optical technology can be utilised to detect endodontic bacterial infection without conventional incubation, allowing clinicians to determine the endpoint of chemomechanical debridement and increase the positive outcomes of RCTs.

Single-cell atlas of dental pulp stem cells exposed to the oral bacteria Porphyromonas gingivalis and Enterococcus faecalis

Introduction: Porphyromonas gingivalis and Enterococcus faecalis promote the development of pulpitis and periapical periodontitis. These bacteria are difficult to eliminate from the root canal systems, leading to persistent infection and poor treatment outcomes. We explored the response of human dental pulp stem cells (hDPSCs) to bacterial invasion and the mechanisms underlying the impact of residual bacteria on dental pulp regeneration. Methods: Single-cell sequencing was used to categorize the hDPSCs into clusters based on their response to P. gingivalis and E. faecalis. We depicted a single-cell transcriptome atlas of hDPSCs stimulated by P. gingivalis or E. faecalis. Results: The most differentially expressed genes in the Pg samples were THBS1, COL1A2, CRIM1, and STC1, which are related to matrix formation and mineralization, and HILPDA and PLIN2, which are related to the cellular response to hypoxia. A cell cluster characterized by high expression levels of THBS1 and PTGS2 was increased after P. gingivalis stimulation. Further signaling pathway analysis showed that hDPSCs prevented P. gingivalis infection by regulating the TGF-β/SMAD, NF-κB, and MAPK/ERK signaling pathways. Differentiation potency and pseudotime trajectory analyses showed that hDPSCs infected by P. gingivalis undergo multidirectional differentiation, particularly to the mineralization-related cell lineage. Furthermore, P. gingivalis can create a hypoxia environment to effect cell differentiation. The Ef samples were characterized by the expression of CCL2, which is related to leukocyte chemotaxis, and ACTA2, which is related to actin. There was an increased proportion of a cell cluster that was similar to myofibroblasts and exhibited significant ACTA2 expression. The presence of E. faecalis promoted the differentiation of hDPSCs into fibroblast-like cells, which highlights the role of fibroblast-like cells and myofibroblasts in tissue repair. Discussion: hDPSCs do not maintain their stem cell status in the presence of P. gingivalis and E. faecalis. They differentiate into mineralization-related cells in the presence of P. gingivalis and into fibroblast-like cells in the presence of E. faecalis. We identified the mechanism underlying the infection of hDPSCs by P. gingivalis and E. faecalis. Our results will improve understanding of the pathogenesis of pulpitis and periapical periodontitis. Furthermore, the presence of residual bacteria can have adverse effects on the outcomes of regenerative endodontic treatment.

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): patients with teeth presenting persistent endodontic infection; C (Concept): microbial profile; and C (Context): 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 one 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 no symptomatology or adequate filling. A greater number of microorganisms was observed in teeth with inadequate coronal restoration compared to adequate restoration.

CONCLUSION

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.

Evaluation of the Oral Bacterial Genome and Metabolites in Patients with Wolfram Syndrome

In Wolfram syndrome (WFS), due to the loss of wolframin function, there is increased ER stress and, as a result, progressive neurodegenerative disorders, accompanied by insulin-dependent diabetes. The aim of the study was to evaluate the oral microbiome and metabolome in WFS patients compared with patients with type 1 diabetes mellitus (T1DM) and controls. The buccal and gingival samples were collected from 12 WFS patients, 29 HbA1c-matched T1DM patients (p = 0.23), and 17 healthy individuals matched by age (p = 0.09) and gender (p = 0.91). The abundance of oral microbiota components was obtained by Illumina sequencing the 16S rRNA gene, and metabolite levels were measured by gas chromatography–mass spectrometry. Streptococcus (22.2%), Veillonella (12.1%), and Haemophilus (10.8%) were the most common bacteria in the WFS patients, while comparisons between groups showed significantly higher abundance of Olsenella, Dialister, Staphylococcus, Campylobacter, and Actinomyces in the WFS group (p < 0.001). An ROC curve (AUC = 0.861) was constructed for the three metabolites that best discriminated WFS from T1DM and controls (acetic acid, benzoic acid, and lactic acid). Selected oral microorganisms and metabolites that distinguish WFS patients from T1DM patients and healthy individuals may suggest their possible role in modulating neurodegeneration and serve as potential biomarkers and indicators of future therapeutic strategies.

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.

Endodontic Microbial Communities in Apical Periodontitis

INTRODUCTION

Apical periodontitis (AP) represents an inflammatory condition of peri-radicular tissues due to invasion and colonization of bacteria in the root canals. Primary apical periodontitis (PAP) is associated with untreated necrotic root canal and can be efficiently treated with endodontic treatment to remove bacteria. Persistent/secondary apical periodontitis (SAP) is a perpetual periapical lesion due to unsuccessfully treated root canals after an initial apparent healing of the tooth. The aim of the study was evaluating the microbial communities associated with root canals using Nanopore sequencing.

METHODS

Seventeen samples from the root canals of 15 patients with AP were Polymerase Chain Reaction-amplified for 16s ribosomal DNA gene and sequenced. Information regarding the presence or absence of AP symptoms, PAP and SAP, and periapical index of patients were recorded.

RESULTS

Firmicutes, Bacteroidetes, and Actinobacteria were the most abundant phyla detected and Phocaeicola, Pseudomonas, Rothia, and Prevotella were the most prominent genera. In samples of patients with AP symptoms, the most frequent detected genera were Cutibacterium, Lactobacillus, Pseudomonas, Dialister, Prevotella, and Staphylococcus. In PAP samples, the most represented genera were Cutibacterium, Lactobacillus, Pseudomonas, and Prevotella, whilst in SAP cases were Cutibacterium, Prevotella, Atopobium, Capnocytophaga, Fusobacterium, Pseudomonas, Solobacterium, and Streptococcus.

CONCLUSIONS

The results provide additional information on the microbiota of root-canals. These data evidence the complexity of the microbiota and the relationship with many clinical and endodontic conditions. Future studies must evaluate these conditions and identify their role in inducing bone damage and local and systemic disease, aiming to better elucidate the relationship between microbes and endodontic pathologies.

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.

Analysis of oral microbiota in non-vital teeth and clinically intact external surface from patients with severe periodontitis using Nanopore sequencing: a case study

Periodontal diseases include a wide range of pathological conditions, damaging the supporting structures of the teeth. Origin and propagation of periodontal disease is believed to be caused by dysbiosis of the commensal oral microbiota. The aim of this study was to evaluate the presence of bacteria in the pulp cavity of teeth with severe periodontal disease with clinically intact external surface. Periodontal (P) and endodontic (E) tissue samples of root canals from six intact teeth of three patients were sampled for analysis of microbial population using Nanopore technology. Streptococcus was the predominant genus in E samples. Porphyromonas (33.4%, p = 0.047), Tannerella (41.7%, p = 0.042), and Treponema (50.0%, p = 0.0064) were significantly more present in P than in E samples. Some samples (E6 and E1) exhibited a remarkable difference in terms of microbial composition, whilst Streptococcus was a common signature in samples E2 to E5, all which were obtained from the same patient. In conclusion, bacteria were identified on both the root surface and the root canal system, thus demonstrating the possibility of bacteria to spread directly from the periodontal pocket to the root canal system even in the absence of crown's loss of integrity.

In vitro antibacterial activity of endodontic bioceramic materials against dual and multispecies aerobic-anaerobic biofilm models

The aim of this in vitro study was to evaluate the antibacterial activity of calcium silicate repair cements and sealers against a dual-species planktonic aerobic model with different aging times and the ability to inhibit the formation of a mature 21-day-old multispecies anaerobic biofilm. The antibacterial activity of ProRoot MTA, MTA Angelus, Biodentine, BioRoot RCS and TotalFill BC sealer against a dual-species aerobic planktonic model, as well as measuring how materials were affected by aging, was evaluated using the Modified Direct Contact Test. Subsequently, the ability to inhibit the formation of a mature multispecies anaerobic biofilm was evaluated using scanning electron microscopy complemented with confocal laser scanning microscopy. Biodentine and BioRoot RCS had higher antibacterial action, and Biodentine was able to maintain its antibacterial action after a prolonged aging period in vitro. Calcium silicate repair cement MTA ProRoot and Biodentine had higher antibiofilm action.

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.

Fucoidan-derived carbon dots against Enterococcus faecalis biofilm and infected dentinal tubules for the treatment of persistent endodontic infections

Enterococcus faecalis (E. faecalis) biofilm-associated persistent endodontic infections (PEIs) are one of the most common tooth lesions, causing chronic periapical periodontitis, root resorption, and even tooth loss. Clinical root canal disinfectants have the risk of damaging soft tissues (e.g., mucosa and tongue) and teeth in the oral cavity, unsatisfactory to the therapy of PEIs. Nanomaterials with remarkable antibacterial properties and good biocompatibility have been developed as a promising strategy for removing pathogenic bacteria and related biofilm. Herein, carbon dots (CDs) derived from fucoidan (FD) are prepared through a one-pot hydrothermal method for the treatment of PEIs. The prepared FDCDs (7.15 nm) with sulfate groups and fluorescence property are well dispersed and stable in water. Further, it is found that in vitro FDCDs display excellent inhibiting effects on E. faecalis and its biofilm by inducing the formation of intracellular and extracellular reactive oxygen species and altering bacterial permeability. Importantly, the FDCDs penetrated the root canals and dentinal tubules, removing located E. faecalis biofilm. Moreover, the cellular assays show that the developed FDCDs have satisfactory cytocompatibility and promote macrophage recruitment. Thus, the developed FDCDs hold great potential for the management of PEIs.

Microbial Communities in the Extraradicular and Intraradicular Infections Associated With Persistent Apical Periodontitis

Microorganisms in the complex root canal system and the extraradicular regions, including the periapical lesions and extraradicular biofilm may cause root canal treatment failures. However, few studies described the difference between the intraradicular and extraradicular infections from the same tooth associated with persistent apical periodontitis. This study aimed to characterize the microbiome present in the root canal, extraradicular biofilm, and periapical lesions associated with persistent apical periodontitis. The microbial communities in the root canal, extraradicular biofilm, and periapical lesions were investigated by Illumina high-throughput sequencing using Illumina Hiseq 2500 platform. The dominant phyla in the extraradicular and intraradicular infections associated with persistent apical periodontitis were Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, and the genera Fusobacterium, Morganella, Porphyromonas, Streptococcus, and Bifidobacterium dominated across all samples. Although extraradicular infection sites showed higher OTU richness and β-diversity compared to intraradicular samples, the occurrence of sinus tract rather than the sampling sites demarcated the microbial communities in the infections associated with persistent apical periodontitis. PERMANOVA analysis confirmed that the samples with or without sinus tracts contained significantly different microbial communities. Porphyromonas, Eubacterium, Treponema, and Phocaeicola were found in significantly higher levels with sinus tracts, whilst Microbacterium and Enterococcus were more abundant in samples without sinus tracts. In conclusion, diverse bacteria were detected in both intraradicular and extraradicular infections associated with persistent apical periodontitis, which might be influenced by the occurrence of the sinus tract. The results may provide new insight into the pathogenesis of persistent apical periodontitis.

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-computed 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.

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.

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.

Local immunomodulatory effects of intracanal medications in apical periodontitis

The immune system is an extremely complex biological network that plays a crucial role in the hemostasis of periapical tissue, pathogenesis of apical periodontitis (AP) as well as periapical tissue healing. The successful elimination of microbial infections remains a significant challenge, mostly due to the ever-growing development of antimicrobial-resistant pathogens. The bacterial endurance in the root canal system contributes to features ranging from altered post-treatment healing to exacerbation of chronic periradicular immune response, that compromise the outcome of endodontic treatment. A highly effective strategy for combating infectious diseases and the associated inflammation-mediated tissue damage is to modulate the host immune response in conjunction with antimicrobial therapy. There are several medications currently used in endodontic treatment, however, they suffer various levels of microbial resistance and do not deliver all the required characteristics to simultaneously address both intracanal bacteria and periapical inflammation. Interaction of antimicrobial agents with the immune system can impact its function, leading to immune-suppressive or immune-stimulatory effects. The group of non-conventional antimicrobial medications, such as antimicrobial peptides, propolis, and nanomaterials, are agents that provide strong antimicrobial effectiveness and concomitant immunomodulatory and/or reparative effect, without any host tissue damages. Herein, we provide an overview of local immune modulation in AP and a comprehensive review of the immunomodulatory effect of antimicrobials intracanal medications applied in endodontics with specific emphasis on the antimicrobial nanomaterial-based approaches that provide immunomodulatory potential for successful clinical deployment in endodontics.

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.

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.

Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next-generation sequencing

AIM

To determine the microorganism in root canal systems of root filled teeth with periapical disease and their relationship with clinical symptoms using next-generation sequencing.

METHODOLOGY

The roots of 10 extracted teeth were collected from 10 patients who presented with post-treatment apical periodontitis (PTAP; six with symptoms and four without symptoms). Each root was divided horizontally into two parts (apical and coronal segments) and cryo-pulverized. Microbial communities were detected using 16S rDNA hypervariable V3-V4 region. The diversity, principal coordinate analysis and linear discriminant analysis effect size were performed in the symptomatic and asymptomatic groups (apical and coronal parts respectively). A Mann-Whitney test and an analysis of similarities were applied for intergroup analysis, at a significance level of 5%.

RESULTS

A total of 23 phyla, 257 genera and 425 species were detected. Firmicutes was the most abundant phylum in all samples. Three phyla (Fusobacteria, Synergistetes and unidentified_Bacteria) and seven genera (Fusobacterium, Porphyromonas, Phocaeicola, Olsenella, Campylobacter, Tannerella and Fretibacterium) were significantly more abundant in the symptomatic patients (p < .05), whereas asymptomatic patients had more Sphingomonas. The species more significantly abundant in the symptomatic samples were Porphyromonas gingivalis, Phocaeicola abscessus, Campylobacter showae, Tannerella forsythia and Olsenella uli (p < .05).

CONCLUSIONS

A greater microbial diversity was observed in root filled teeth with PTAP compared to earlier reports. Several genera and species in root canal systems might be associated with clinical symptoms of PTAP.

Antibacterial Activity of Copper Nanoparticles (CuNPs) against a Resistant Calcium Hydroxide Multispecies Endodontic Biofilm

Endodontic treatment reduces the amount of bacteria by using antimicrobial agents to favor healing. However, disinfecting all of the canal system is difficult due to its anatomical complexity and may result in endodontic failure. Copper nanoparticles have antimicrobial activity against diverse microorganisms, especially to resistant strains, and offer a potential alternative for disinfection during endodontic therapy. This study evaluated the antibacterial action of copper nanoparticles (CuNPs) on an ex vivo multispecies biofilm using plaque count compared to the antibacterial activity of calcium hydroxide Ca(OH)₂. There were significant differences between the Ca(OH)₂ and CuNPs groups as an intracanal dressing compared with the CuNPs groups as an irrigation solution (p < 0.0001). An increase in the count of the group exposed to 7 days of Ca(OH)₂ was observed compared to the group exposed to Ca(OH)₂ for 1 day. These findings differ from what was observed with CuNPs in the same period of time. Antibacterial activity of CuNPs was observed on a multispecies biofilm, detecting an immediate action and over-time effect, gradually reaching their highest efficacy on day 7 after application. The latter raises the possibility of the emergence of Ca(OH)₂-resistant strains and supports the use of CuNPs as alternative intracanal medication.

Oral Sampling Techniques

The human oral cavity is a major point of entry for microorganisms, many of which live and multiply in the mouth. In addition, it provides an accessible site for sampling compared to other parts of the body; however, caution should be taken during oral sampling as many factors contribute to the microbial diversity in a site-dependent manner. The accessibility of the oral cavity and its microbial diversity emphasize the crucial need to avoid cross-contamination during the sampling procedure. In this chapter, we describe various detailed oral sampling procedures. These methods include supragingival dental plaque sampling, subgingival dental plaque sampling, oral mucosal sampling, and endodontic sampling methods for extracted teeth or in the patient's mouth. The proposed protocols provide tips to avoid contamination between different oral sources of bacteria and possible alternatives to the tools used.

Diverse microbiota in palatal radicular groove analyzed by Illumina sequencing: Four case reports

BACKGROUND

A palatal radicular groove is an unusual developmental deformity of the tooth, which may serve as a channel linking the periodontal and periapical inflammation, and yet no literature could be obtained analyzing microbiota within the palatal radicular grooves.

CASE SUMMARY

Four patients diagnosed with palatal radicular groove and concomitant periodontal-endodontic deformity in permanent maxillary lateral incisors were enrolled in this work. Twelve bacterial samples from 4 patients were collected from different parts of the palatal radicular groove during intentional replantation surgery. Illumina sequencing was performed to analyze the taxonomical composition and microbiome structure inside the palatal grooves, and 1162 operational taxonomic units were obtained. The phyla of Firmicutes and Proteobacteria predominated in most of the samples. An unknown genus from the Bacillaceae family, Lactococcus, and Porphyromonas were the most abundant genera identified. There was no difference in the microbiota richness and diversity in three sections of the groove.

CONCLUSION

The unique ecological niches inside the palatal grooves harbored bacterial communities that shared some component features of both the endodontic and periodontal infections. The existence of palatal groove may play an interaction bridge between the root apex and tooth cervix and thus impair the outcome of traditional therapeutic methods such as root canal treatment and periodontal management.

APORTES Y DIFICULTADES DE LA METAGENÓMICA DE SUELOS Y SU IMPACTO EN LA AGRICULTURA

Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.

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.

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.

Doxycycline-functionalized polymeric nanoparticles inhibit Enterococcus faecalis biofilm formation on dentine

AIM

To evaluate in a laboratory setting the antimicrobial properties and the potential to inhibit biofilm formation of novel remineralizing polymeric nanoparticles (NPs) when applied to dentine surfaces and to ascertain the effect of the functionalization of these NPs with zinc, calcium or doxycycline.

METHODOLOGY

The antimicrobial activity and inhibition of biofilm formation of polymeric NPs were analysed on human dentine blocks that were infected with Enterococcus faecalis before or after application of NPs. LIVE/DEAD ® testing under Confocal Laser Scanning Microscopy and bacterial culturing were employed to analyse biofilm biovolume and bacterial viability. Field Emission Scanning Electron Microscopy was also employed to assess biofilm morphology. One-way anova with Welch's correction and post hoc comparison by the Games-Howell test were performed for comparisons between groups.

RESULTS

The un-functionalized NPs displayed the greatest antimicrobial activity against E. faecalis biofilms as they provided the lowest biovolume (3865.7 ± 2926.97 µm³ ; P < 0.001) and the highest dead/injured cells percentage (79.93 ± 18.40%; P < 0.001), followed by Dox-NPs (biovolume: 19,041.55 ± 17,638.23 µm³ , dead/injured cells: 45.53 ± 26.50%; P < 0.001). Doxycycline-loaded NPs had the largest values of inhibition of biofilm formation with the lowest biofilm biovolume (8517.65 ± 7055.81 µm³ ; P < 0.001) and a high dead/injured bacterial percentage (68.68 ± 12.50%; P < 0.001). Un-functionalized NPs did not reduce biomass growth (P > 0.05), but attained the largest percentage of compromised cells (93 ± 8.23%; P < 0.001), being able to disrupt biofilm formation. It also produced occlusion of dentinal tubules, potentially interfering with bacterial tubule penetration.

CONCLUSIONS

A new generation of bioactive nano-fillers (doxycycline-functionalized polymeric NPs) had antibacterial activity and occluded dentinal tubules. Incorporating these NPs into endodontic sealers may have the potential to enhance the outcome of root canal treatment.

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.

Detection, treatment and prevention of endodontic biofilm infections: what's new in 2020?

Endodontic disease, a biofilm infection of the root canal space, is a significant cause of dental morbidity worldwide. Endodontic treatment, or root canal treatment, as it is commonly known is founded on the ability to eradicate microbial biofilm infection and prevent re-infection of the highly complex root canal space. Despite many "advances" in clinical endodontics we have seen little improvement in outcomes. The aim of this critical review paper is to provide a contemporary view of endodontic microbiology and biofilm polymicrobiality, provide an understanding of the host response, and how together these impact upon clinical treatment. Ultimately, it is intended to provide insight into novel opportunities and strategies for the future diagnostics, treatment, and prevention of endodontic disease.

Age-dependent root canal instrumentation techniques: a comprehensive narrative review

The aim of this article was to review age-dependent clinical recommendations for appropriate root canal instrumentation techniques. A comprehensive narrative review of canal morphology, the structural characteristics of dentin, and endodontic outcomes at different ages was undertaken instead of a systematic review. An electronic literature search was carried out, including the Medline (Ovid), PubMed, and Web of Science databases. The searches used controlled vocabulary and free-text terms, as follows: 'age-related root canal treatment,' 'age-related instrumentation,' 'age-related chemo-mechanical preparation,' 'age-related endodontic clinical recommendations,' 'root canal instrumentation at different ages,' 'geriatric root canal treatment,' and 'pediatric root canal treatment.' Due to the lack of literature with practical age-based clinical recommendations for an appropriate root canal instrumentation technique, a narrative review was conducted to suggest a clinical algorithm for choosing the most appropriate instrumentation technique during root canal treatment. Based on the evidence found through the narrative review, an age-related clinical algorithm for choosing appropriate instrumentation during root canal treatment was proposed. Age affects the morphology of the root canal system and the structural characteristics of dentin. The clinician's awareness of root canal morphology and dentin characteristics can influence the choice of instruments for root canal treatment.

Phages in a thermoreversible sustained-release formulation targeting E. faecalis in vitro and in vivo

Introduction

Enterococcus faecalis is a key pathogen recovered from root canals when conventional treatment fails. Phage therapy has generated new interest in combating pathogens. A sustained-release formulation using specific phages against E. faecalis may offer an alternative approach.

Objectives

To evaluate the efficacy of anti-E. faecalis phages formulated in a thermo- sustained-release system against E. faecalis in vitro and in vivo.

Methods

EFDG1 and EFLK1 phages were formulated with poloxamer P407. Gelation time, phage survival, activity and toxicity were evaluated. Lytic activity was evaluated in vitro against E. faecalis at various growth phases, including anti-biofilm activity. Methods included viable bacterial count (CFU/mL), biofilm biomass determination and electron microscopy (live/dead staining). Further evaluation included infected incisors in an in vivo rat model. Anti-E. faecalis phage-cocktail suspension and sustained-release phage formulation were evaluated by viable bacterial count (CFU/mL), histology, scanning electron microscopy (SEM) and 16S genome sequencing of the microbiota of the root canal.

Results

Gelation time for clinical use was established. Low toxicity and a high phage survival rate were recorded. Sustained-release phages reduced E. faecalis in logarithmic (4 logs), stationary (3 logs) and biofilm (4 logs) growth phases. Prolonged anti-biofilm activity of 88% and 95% reduction in biomass and viable counts, respectively, was recorded. Reduction of intracanal viable bacterial counts was observed (99% of enterococci) also seen in SEM. Phage treatment increased Proteobacteria and decreased Firmicutes. Histology showed reduced periapical inflammation and improved healing following phage treatment.

Conclusion

Poloxamer P407 formulated with phages has an effective and long-lasting effect in vitro and in vivo targeting E. faecalis.

Inspection of the Microbiota in Endodontic Lesions

The primary objective of endodontic therapy is to create a biologically acceptable environment within the root canal system that allows for the healing and maintenance of the health of the peri-radicular tissue. Bacteria are one of the main causes of pulp problems, and they have different methods of penetrating and invading the endodontic space such as through carious lesions, traumatic pulp exposures, and fractures. The types of bacteria found range from facultative anaerobes to aerobes, up to the most resistant species able to survive in nutrient-free environments; the bacterial species Enterococcus faecalis belongs to this last group. Enterococcus faecalis is considered one of the main causes of recurring apical periodontal lesions following endodontic treatment, with persistent lesions occurring even after re-treatment. The review presented in this paper was performed in accordance with the PRISMA protocol and covers articles from the related scientific literature that were sourced from PubMed, Scopus, and Google Scholar using the following terms as keywords: “endodontic treatment”, “endodontic bacteria”, “microbial endodontic”, and “endodontic failure”. Only the articles considered most relevant for the purposes of this paper were read in full and taken into consideration for the following review. The results show that Enterococcus faecalis, Actinomycetes, and Propionibacterium propionicum are the species most frequently involved in persistent radicular and extra-radicular infections.

Historical and Contemporary Perspectives on the Microbiological Aspects of Endodontics

The microbiota of the oral cavity plays a significant role in pulpal and periapical diseases. Historically, 100 years ago little was known on microbiota, but after a century of investigations, only now can many of the intimate secrets of microbial growth, expansion, persistence, communal activities, and virulence be revealed. However, with the capabilities of the microbiota for mutation, quorum sensing, and information transference, researchers are hard-pressed to keep up with both the changes and challenges that an amazingly wide range of bacterial species pose for both the scientist and clinician. Fortunately, the development and expansion of a vast array of molecular biological investigative techniques have enabled dentistry and its associated medical fields to attempt to keep pace with the wide and fascinating world of oral microbiology.