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

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.

Identification of bacteria associated with periapical abscesses of primary teeth by sequence analysis of 16S rDNA clone libraries

OBJECTIVE

This study aims to detect the predominant bacteria in acute periapical abscesses of primary teeth using culture-independent molecular methods based on 16S ribosomal DNA cloning.

METHODS

Purulent material was collected from nine children diagnosed with abscesses of endodontic origin. DNA was extracted and the 16S rRNA gene amplified with universal primer pairs 27F and 1492R. Amplified genes were cloned, sequenced by Applied Biosystems, and identified by comparison with known 16S rRNA gene sequences.

RESULTS

Bacterial DNA was present in all nine purulence samples. A total of 681 clones were classified into 8 phyla, 78 genera, and 125 species/phylotypes. The phyla were Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Tenericutes, Deinococcus-Thermus, and Spirochaetes. The most dominant genera were Streptococcus (13.3%), Fusobacterium (11.8%), Parvimonas (7.8%), Prevotella (6.7%), Sphingomonas (5.8%), and Hafnia (5.2%). Fusobacterium nucleatum (11.5%), Parvimonas micra (7.8%), Streptococcus intermedius (6.6%), Sphingomonas echinoides (5.3%), Hafnia alvei (5.2%), and Citrobacter freundii (4.9%) were the most common species/phylotypes. Among these species/phylotypes, F.nucleatum was the most prevalent (7/9). C. freundii, Carnobacterium maltaromaticum, and H. alvei were seldom detected species in acute periapical abscesses but had relatively high abundance and prevalence.

CONCLUSION

Acute periapical abscesses are polymicrobial with certain prevalent bacteria, especially anaerobic bacterium. The most predominant and prevalent bacteria of acute periapical abscesses in children was F. nucleatum.

Characteristics of the salivary microbiota in cheilitis granulomatosa

Background

Cheilitis granulomatosa (CG) is a disturbing and persistent idiopathic lip swelling. The cause and treatment has not been wholly elucidated. Some reports infer that CG is mainly associated with dental infection but no firm or reliable microbiological evidence has been provided for a causative organism. This study aimed to evaluate whether microorganisms contribute to the etiology of CG in order to inform appropriate treatment options in clinic.

Material and Methods

Unstimulated saliva was collected from 15 CG patients who were diagnosed clinically and pathologically and 15 healthy controls (HC). DNA was extracted from the precipitate of the centrifuged saliva for 16s rRNA high-throughput sequencing using the Miseq PE300 platform. The distribution of the microbiome between the two groups was compared.

Results

CG patients had a greater microbial flora that was more diverse than the HC. Prevotella, Alloprevotella, Porphyromonas, Actinomyces, Rothia, Fusobacterium, Haemophilus, and Aggregatibacter had a significantly higher abundance in CG patients. In contrast, Streptococcus and Campylobacter were the most abundant genera in HC with a mean relative abundance of 63% and 2%, respectively. The microbiological network indicated that most of the bacteria that were enriched at greater levels in CG patients were likely to be Prevotella, Actinomyces, and Rothia. These have been shown to co-exist with other bacteria.

Conclusions:

The composition and structure of bacterial communities in CG patients were different from HC. Most of the genera observed in CG patients were associated with periodontitis and pulp infection. These findings might be helpful in understanding the etiology of CG. Further study will be needed to confirm these findings and explore the underlying pathological mechanism.

Key words:Cheilitis granulomatosa, 16s rRNA high-throughput sequencing, salivary microbiota.

Significance of oral health in adult patients with congenital heart disease

Due to improved diagnosis and treatment life expectancy of patients with congenital heart disease is steadily increasing resulting in a growing portion of adult patients. When entering, adulthood patients commonly show a shift in their specific needs for medical care. Since the treatment is mostly not curative many patients have life-long cardiovascular anomalies, among others, entailing high risk for the development of infective endocarditis. Several oral diseases, i.e., caries, apical periodontitis and periodontitis show a very high overall prevalence. These entities are primarily initiated by bacterial infections. Hence, they cause an inherent risk for bacteremia and subsequently for infective endocarditis in patients with congenital heart disease during professional dental care and various daily activities. Conversely congenital heart disease seems to be inevitably associated with considerable impairment of oral health resulting in a tight interrelation between both entities. Different preventive strategies are available to address the elevated risk for infective endocarditis due to oral diseases in patients with congenital heart disease during professional dental care and routine daily activities. This review delineates the current evidence regarding the issue of oral health in adult patients with congenital heart disease.

Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis

Opportunistic bacteria in apical periodontitis (AP) may pose a risk for systemic dissemination. Mucosal-associated invariant T (MAIT) cells are innate-like T cells with a broad and potent antimicrobial activity important for gut mucosal integrity. It was recently shown that MAIT cells are present in the oral mucosal tissue, but the involvement of MAIT cells in AP is unknown. Here, comparison of surgically resected AP and gingival tissues demonstrated that AP tissues express significantly higher levels of Vα7.2-Jα33, Vα7.2-Jα20, Vα7.2-Jα12, Cα and tumour necrosis factor (TNF), interferon (IFN)-γ and interleukin (IL)-17A transcripts, resembling a MAIT cell signature. Moreover, in AP tissues the MR1-restricted MAIT cells positive for MR1–5-OP-RU tetramer staining appeared to be of similar levels as in peripheral blood but consisted mainly of CD4⁺ subset. Unlike gingival tissues, the AP microbiome was quantitatively impacted by factors like fistula and high patient age and had a prominent riboflavin-expressing bacterial feature. When merged in an integrated view, the examined immune and microbiome data in the sparse partial least squares discriminant analysis could identify bacterial relative abundances that negatively correlated with Vα7.2-Jα33, Cα, and IL-17A transcript expressions in AP, implying that MAIT cells could play a role in the local defence at the oral tissue barrier. In conclusion, we describe the presence of MAIT cells at the oral site where translocation of oral microbiota could take place. These findings have implications for understanding the immune sensing of polymicrobial-related oral diseases.

Influence of microbiology on endodontic failure. Literature review

BACKGROUND

The main cause of endodontic failure is the persistence of microorganisms that cause an intraradicular or extratradicular infection and that become resistant to disinfection measures. The objective of this review is to identify the microbiota associated with endodontic failure, as well as the reasons why these microorganisms are capable of surviving basic disinfection measures.

MATERIAL AND METHODS

Systematic search of scientific articles in the databases PubMed with the following keywords "Endodontic Infections", "Endodontic Microbiology", "Endodontic Failure", "Enterococcus Faecalis", "Endodontics Retreatment" was carried out. Case reports and articles with publication date prior to 2000 were not included in this review.

RESULTS

Most authors highlight E. faecalis as the main microorganism associated with endodontic failure, nevertheless there are recent studies that isolate, to a greater extent, other bacteria such as Fusobacterium nucleatum and Propionibacterium.

DISCUSSION

These microorganisms have in common the following proprieties, which make them able to escape the disinfection measures: the ability to form a biofilm, to locate in areas unreachable to root canal instrumentation techniques, synergism, the ability to express survival genes and activate alternative metabolic pathways.

Microbiota in the apical root canal system of tooth with apical periodontitis

Background

Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral.

Methods

Four groups of specimens are considered, the apical part of root from diseased teeth with and without root canal treatment, and wisdom teeth extracted to avoid being impacted (tooth healthy control), as well as an additional healthy oral control from biofilm of the buccal mucosa. DNA was extracted from these specimens and the microbiome was examined through focusing on the V3-V4 hypervariable region of the 16S rRNA gene using sequencing on Illumina MiSeq platform. Composition and diversity of the bacterial community were tested for individual samples, and between-group comparisons were done through differential analysis to identify the significant changes.

Results

We observed reduced community richness and diversity in microbiota samples from diseased teeth compared to healthy controls. Through differential analysis between AP teeth and healthy teeth, we identified 49 OTUs significantly down-regulated as well as 40 up-regulated OTUs for AP.

Conclusion

This study provides a global view of the microbial community of the AP associated cohorts, and revealed that AP involved not only bacteria accumulated with a high abundance, but also those significantly reduced ones due to microbial infection.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5474-y) contains supplementary material, which is available to authorized users.

Inflammatory potential of monospecies biofilm matrix components

AIM

To assess the inflammatory potential of biofilm matrix constituents of Enterococcus faecalis and Pseudomonas aeruginosa monospecies biofilms on macrophages.

METHODOLOGY

In vitro biofilms of E. faecalis and P. aeruginosa were grown (7 days) in aerobic and anaerobic conditions. The biofilm matrix components: exopolysaccharides (EPS) and extracellular DNA (eDNA) were extracted and quantified. The inflammatory potential of EPS and eDNA was assessed on macrophage cell lines (RAW 267.4) using nitric oxide (NO), and enzyme-linked immunosorbent assay for tumour necrosis factor (TNF-α) and interleukin-6 (IL-6) expressions. LPS from P. aeruginosa and planktonic bacteria were positive controls. One-way analysis of variance and the Tukey post hoc test were used for statistical analysis.

RESULTS

Extracted EPS from both biofilm strains was associated with higher levels than eDNA in both growth conditions (P < 0.05). The biofilm components had less inflammatory potential compared to planktonic bacteria and LPS. EPS produced higher levels of inflammatory response compared to eDNA for both strains (P < 0.05). IL-6 and TNF-α, and NO expression showed no difference for E. faecalis EPS (P ≥ 0.05). In contrast, P. aeruginosa EPS and eDNA had significant levels of IL-6 compared to TNF-α and NO (P < 0.05).

CONCLUSIONS

Monospecies biofilm matrix EPS and eDNA from the bacterial strains tested had the ability to induce a low-grade inflammatory response when compared to planktonic bacteria and LPS. This study highlights the potential of biofilm matrix/components, devoid of bacteria to induce low-grade chronic inflammation.

Pro-inflammatory and anti-inflammatory cytokine expression in post-treatment apical periodontitis

OBJECTIVE

This study evaluated the expression of pro-inflammatory (IL-1β, IL-6, IFN-γ and TNF-α) and anti-inflammatory (IL-4 and TGF-β) cytokines in apical periodontitis lesions. Correlations between these cytokines and clinical and cone-beam computed tomographic (CBCT) data were also assessed.

MATERIAL AND METHODS

Apical periodontitis lesions' data were obtained from 27 patients subjected to periradicular surgery. Specimens were processed for histopathologic and immunohistochemical analysis. Sections were evaluated according to the amount of positive staining for each antibody. Expression levels of the target mediators were compared with clinical and CBCT data.

RESULTS

Twenty lesions were diagnosed as granuloma and 7 as cyst. In granulomas, IL-4 expression was significantly higher than IL-6 (p=0.001) and TNF-α (p=0.001). There was a significant relationship between high levels of TNF-α and lesions <5 mm (p=0.017). In cysts, IL-6 expression was significant lower than IL-4 (p=0.001) and IFN-γ (p=0.004). There was a significant relationship between high levels of TGF-β and endodontic treatment performed ≤4 years before (p=0.045). In general, IL-4 was the most expressed mediator in both cysts and granulomas.

CONCLUSIONS

There was a balance between the expression of pro-inflammatory and anti-inflammatory cytokines associated with the chronic periradicular inflammatory process. TNF-α and TGF-β were related to some clinical and CBCT data.

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

AIM

To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS).

METHODOLOGY

Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data.

RESULTS

A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients.

CONCLUSIONS

Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.

Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt

The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level, Prevotella, Bacillus, Porphyromonas, Streptococcus, and Bacteroides were the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis

Introduction

Acute apical abscess is caused by bacteria that leave the infected dental root canal to invade the periodontal tissues. Most species occurring in abscesses are also found in asymptomatic infections; therefore, the possibility exists that not only the presence of certain species but also their specific counts influence the appearance of symptoms. This molecular study compared the frequency and levels of several candidate endodontic pathogens in teeth with acute apical abscesses and asymptomatic apical periodontitis.

Methods

Samples were taken from the root canals of teeth with asymptomatic apical periodontitis (n = 73) and by aspiration of purulent exudate from acute abscesses (n = 55). DNA was extracted from samples and bacterial identifications were performed by a closed-ended semi-quantitative reverse-capture checkerboard approach targeting 40 bacterial species/phylotypes.

Results

Bacterial DNA was detected in all cases. In abscesses, the most prevalent taxa were Fusobacterium nucleatum (60%), Porphyromonas endodontalis (53%), Parvimonas micra (51%), and Streptococcus species (45%). The most frequently detected taxa in asymptomatic teeth were P. endodontalis (63%), Dialister invisus (58%), Olsenella uli (56%), and F. nucleatum (51%). None of the targeted taxa were significantly associated with abscesses when only mere presence was evaluated (p>0.05). However, semi-quantitative data demonstrated that P. endodontalis, Prevotella baroniae, Treponema denticola and Streptococcus species were significantly more frequent at levels >10⁵ in abscesses than in asymptomatic cases (p<0.05).

Conclusion

None of the target species/phylotypes were associated with abscesses in terms of frequency. However, some taxa were significantly found in higher levels in abscesses. Presence of a potentially virulent pathogen in high counts may increase the collective pathogenicity of the bacterial community and give rise to symptoms.

Aging effects in the expression of macrophages in post-treatment apical periodontitis lesions

OBJECTIVES

To evaluate the CD68 immunoexpression in post-treatment apical periodontitis lesions of older patients and compare them with lesions of younger/middle age adults.

METHODS

Biopsy specimens from 21 apical periodontitis lesions (12 granulomas and 9 cysts) were selected from older patients and 25 apical periodontitis lesions from younger/middle age adults (12 cysts and 13 granulomas) were selected and analyzed by immunohistochemistry using silanized slides with anti-CD68 antibody. The slides were subdivided in five high-power fields and the images were observed under an optical microscope to evaluate the epithelial and connective tissues.

RESULTS

The results showed that there was no statistical difference for the CD68 expression in epithelial tissue of cysts between younger/middle age adults and older patients. However, for the connective tissue of both cysts and granulomas, there was a statistical difference between the two age groups. There was a statistical difference between the epithelial and the connective tissues in cysts of younger/middle age adults, and also when the epithelial tissue of the cysts was compared with connective tissue of the granuloma. In the group of older patients, there was no statistical difference between the connective tissue of the cysts and granulomas.

CONCLUSION

The intensity of the macrophage staining was greater in the connective tissue of cysts and granulomas alike in the younger/middle age adult patients, suggesting that these cells participate actively in this tissue. Immune responses in older patients may be compromised, suggesting that there is a greater tendency for the endodontic treatment of these patients to fail.

Radiologic assessment of quality of root canal fillings and periapical status in an Austrian subpopulation - An observational study

Background/Objective

Progress in endodontic techniques and methodological advances have altered root canal therapy over the last decades. These techniques and methods need periodical documentation. This observational study determined the current prevalence of endodontic treatments, and investigated the relationship of various factors with the periapical status in a Lower Austrian subpopulation.

Methodology

One thousand orthopantomograms of first-time university adult patients radiographed at an outpatient clinic were evaluated. For each tooth, the presence of periradicular pathosis and/or endodontic treatment was recorded, as was the quality of (post-)endodontic treatment (homogeneity and length of root canal fillings; preparation failures; posts/screws; apicoectomies; coronal restorations). Two evaluators, blinded to each other, scored all teeth. In cases of disagreement, they joined for a consensus score.

Results

In all, 22,586 teeth were counted. Of these, 2,907 teeth (12.9%) had periapical pathosis, while 2,504 teeth had undergone root canal treatment. Of the endodontically treated teeth, 52% showed no radiographic signs of apical periodontitis, while 44.9% had overt apical lesions, and 3,1% revealed widened periodontal ligament space. The majority of the root canal fillings was inhomogeneous (70.4%); 75.4% were rated too short, and 3.8% too long. The presence of apical pathosis was significantly correlated (odds ratio (OR) 2.556 [confidence interval (CI) 2.076–3.146]; P<0.0001) with poor root canal fillings (length and homogeneity). Posts or screws positively affected periapical status (OR 1.853 [CI 1.219–2.819]; P = 0.004), but endodontically treated posterior teeth were infrequently restored (posts, 7.5%; screws, 2.7%). Best results were found for teeth with both appropriate endodontic treatment and adequate coronal restoration.

Conclusion

A high prevalence of periradicular radiolucencies was observed with root canal filled teeth, along with high numbers of unmet treatment needs. Periapical health was associated with adequate root canal obturation and high-grade postendodontic restorations, and quality regarding these latter aspects is considered mandatory to promote periapical health.