Oral treponemes in primary root canal infections as detected by nested PCR

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

OBJECTIVES

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

MATERIALS AND METHODS

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

RESULTS

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

CONCLUSIONS

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

CLINICAL RELEVANCE

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

Post-Operative Endodontic Pain Management: An Overview of Systematic Reviews on Post-Operatively Administered Oral Medications and Integrated Evidence-Based Clinical Recommendations

Endodontic treatment comprises the overall management of pre-, intra- and post-operative symptoms, including post-operative endodontic pain, considered as a complication susceptible of chronicization. Post-operative pain is very common and highly unpreventable and has a multi-factorial etiology and a potential pathogenic link to the acute inflammation of the periapical area, secondary to localized chemical, mechanical, host and/or microbial damage occurring during endodontic treatment. Considering the multitude of heterogeneous technical and pharmacological approaches proposed to control post-operative endodontic pain, the present study primarily comprised an overview of systematic reviews of systematic reviews of randomized clinical trials, summarizing findings on post-operatively administered oral medications for post-operative endodontic pain control, in order to note the most effective type and dosage of such drugs. Secondarily, a narrative review of the current evidence on technical solutions to be observed during endodontic treatment procedures, to control post-operative pain, was conducted to provide integrated evidence-based clinical recommendations for optimal post-operative endodontic pain management.

Prevalence of red and orange microbial complexes in endodontic-periodontal lesions: a systematic review and meta-analysis

OBJECTIVE

This systematic review assesses the prevalence of microbial complexes in endodontic-periodontal lesion.

MATERIALS AND METHODS

Nine databases were searched through August 2020. Experts were consulted to indicate additional studies. Studies were blindly selected by two reviewers based on pre-defined eligibility criteria. Studies that evaluated the prevalence of microbial orange and red complexes among patients with endodontic-periodontal lesion were considered eligible. Risk of bias was assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Studies Reporting Prevalence Data.

RESULTS

From 572 articles found on all databases, 11 clinical studies were finally included. The following microorganisms were investigated: P. gingivalis, T. forsythia, T. denticola, F. nucleatum, F. periodonticum, P. micra, P. intermedia, P. nigrescens, S. constellatus, C. gracilis, C. rectus, C. showae and E. nodatum. Considering the orange complex, P. micra, E. nodatum and S. constellatus were prevalent in both root canal and periodontal pockets. P. gingivalis and T. forsythia belonging to the red complex were prevalent only in periodontal pockets. The red complex microorganisms were not found very frequently in root canal.

CONCLUSIONS

There is a similarity between the microbiome of root canal and periodontal pockets, with prevalence of the three microorganisms of the orange complex. Two microorganisms from the red complex were prevalent only in periodontal pockets.

CLINICAL RELEVANCE

The prevalence of specific microorganisms in endodontic-periodontal lesion is important to understand the microbiological profile of the patients involved and to correlate it with possible clinical and repair conditions of this pathology.

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.

Assessment of the antibacterial, antivirulence, and action mechanism of Copaifera pubiflora oleoresin and isolated compounds against oral bacteria

The microorganisms that constitute the oral microbiome can cause oral diseases, including dental caries and endodontic infections. The use of natural products could help to overcome bacterial resistance to the antimicrobials that are currently employed in clinical therapy. This study assessed the antimicrobial activity of the Copaifera pubiflora oleoresin and of the compounds isolated from this resin against oral bacteria. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays provided values ranging from 6.25 to > 400 μg/mL for the C. pubiflora oleoresin and its isolated compounds. The fractional inhibitory concentration index (FICI) assay showed that the oleoresin and chlorhexidine did not act synergistically. All the tested bacterial strains formed biofilms. MICB₅₀ determination revealed inhibitory action: values varied from 3.12-25 μg/mL for the oleoresin, and from 0.78 to 25 μg/mL for the ent-hardwickiic acid. Concerning biofilm eradication, the C. pubiflora oleoresin and hardwickiic acid eradicated 99.9 % of some bacterial biofilms. Acid resistance determination showed that S. mutans was resistant to acid in the presence of the oleoresin and ent-hardwickiic acid at pH 4.0, 4.5, and 5.0 at all the tested concentrations. Analysis of DNA/RNA and protein release by the cell membrane demonstrated that the oleoresin and hardwiickic acid damaged the bacterial membrane irreversibly, which affected membrane integrity. Therefore, the C. pubiflora oleoresin and ent-hardwickiic acid have potential antibacterial effect and can be used as new therapeutic alternatives to treat oral diseases such as dental caries and endodontic infections.

Novel Bacterial Phylotypes in Endodontic Infections

Although molecular studies have revealed potential oral pathogens among the phyla Spirochaetes and Deferribacteres, their occurrence in endodontic infections has not been consistently investigated. In this study, we devised a nested PCR-DGGE approach to survey samples from infected root canals for the presence of members of these two phyla, and to examine their diversity. The primers used also amplified DNA from Atopobium species. Eight of 10 cases showed bands representative of the target bacterial groups. DGGE profiles revealed a mean number of 6.5 intense and faint bands. No single band occurred in all profiles. Sequences from intense bands excised from the gel showed similarities to species/phylotypes of all target groups— Flexistipes species ( Deferribacteres phylum), uncharacterized spirochetes, and Atopobium species. Analysis of these data indicates that uncultivated Spirochaetes and Deferribacteres phylotypes are frequent members of the endodontic microbiota and may be potential pathogens involved with the etiology of periradicular diseases.

Isolation of digital dermatitis treponemes from hoof lesions in Wild North American Elk (Cervus elaphus) in Washington State, USA

Since 2008, a large increase in the numbers of cases of lameness have been seen in wild North American elk (Cervus elaphus) from Washington State, USA. The most recent cases manifested as foot lesions similar both clinically and pathologically to those seen in digital dermatitis (DD) in cattle and sheep, a disease with a bacterial etiopathogenesis. To determine whether the same bacteria considered responsible for DD are associated with elk lameness, lesion samples were subjected to bacterial isolation studies and PCR assays for three phylogroups of relevant DD treponemes. The DD treponemes were isolated from lesional tissues but not from control feet or other areas of the diseased foot (including the coronary band or interdigital space), suggesting that the bacteria are strongly associated with DD lesions and may therefore be causal. In addition, PCR analysis revealed that all three unique DD treponeme phylotypes were found in elk hoof disease, and in 23% of samples, all 3 DD-associated treponemes were present in lesions. Sequence analysis of the 16S rRNA gene showed that the elk lesion treponemes were phylogenetically almost identical to those isolated from cattle and sheep DD lesions. The isolates were particularly similar to two of the three culturable DD treponeme phylotypes: specifically, the Treponema medium/Treponema vincentii-like and Treponema phagedenis-like DD spirochetes. The third treponeme culturable phylogroup (Treponema pedis), although detected by PCR, was not isolated. This is the first report describing isolation of DD treponemes from a wildlife host, suggesting that the disease may be evolving to include a wider spectrum of cloven-hoofed animals.

Clinical investigation of bacterial species and endotoxin in endodontic infection and evaluation of root canal content activity against macrophages by cytokine production

INTRODUCTION

This study investigated the presence of different Gram-negative bacterial species and the levels of endotoxins found in primary endodontic infection (PEI), determining their stimulation ability against macrophages through the levels of interleukin (IL)-1, IL-6, IL-10, and tumor necrosis factor alpha (TNF-α), and evaluated their relationship with clinical and radiographic findings.

MATERIAL AND METHODS

Samples were taken from 21 root canals with primary endodontic infection with apical periodontitis (PEIAP). Molecular techniques were used for bacterial detection. Limulus amebocyte lysate assay was used to measure endotoxins. Pro-inflammatory cytokines were measured by ELISA assay.

RESULTS

All samples were positive for bacterial DNA (21/21). Prevotella nigrescens (57.2 %) was the most frequent species. Higher levels of endotoxins were found in teeth with pain on palpation and exudation (all p < 0.05). Positive correlations were found between endotoxins and the levels of TNF-α and IL-1β, whereas a negative correlation was found between endotoxin and the amount of IL-10 (p < 0.05). Endotoxin levels were found to be a risk factor for exudation and increased the number of Gram-negative bacterial species for the presence of a larger area of bone destruction (all p < 0.05).

CONCLUSION

A wide variety of Gram-negative bacterial species are involved in primary endodontic infection, with participation of different Treponema species. Thus, the levels of endotoxins and the number of Gram-negative bacteria species present in root canals were considered risk factors for the severity of endodontic infection.

CLINICAL RELEVANCE

The present study revealed that Gram-negative bacterial species and endotoxins play an important role in the development of signs/symptoms and the severity of bone destruction, this knowledge is essential for the establishment of an effective therapy.

Comparison of endotoxin levels found in primary and secondary endodontic infections

INTRODUCTION

This clinical study was conducted to compare the levels of endotoxins (lipopolysaccharides [LPSs]) found in primary and secondary endodontic infections with apical periodontitis by correlating LPS contents with clinical/radiographic findings. In addition, the presence of target gram-negative anaerobic bacteria was also investigated.

METHODS

Samples were taken from 15 root canals with primary infections and 15 with secondary infections by using paper points. The limulus amebocyte lysate assay was used to quantify endotoxins, and the polymerase chain reaction technique (16S rDNA) was used for bacterial investigation.

RESULTS

Endotoxins were detected in 100% of the root canal samples collected from primary (15/15) and secondary (15/15) infections with median values of 7.49 EU/mL and 3.96 EU/mL, respectively (P < .05). The median value of endotoxins found in the presence of clinical symptoms was significantly higher than in asymptomatic teeth with primary infections (P < .05). A positive correlation was found between endotoxin contents and a larger size of the radiolucent area (>3 mm) (P < .05). Prevotella nigrescens (10/15, 4/15), Fusobacterium nucleatum (5/15, 1/15), Treponema denticola (3/15, 1/15), and Treponema socranskii (5/15, 1/15) were detected in teeth with primary and secondary infections, respectively. P. endodontalis was present only in teeth with primary infections (5/15).

CONCLUSIONS

Teeth with primary endodontic infections had higher contents of endotoxins and a more complex gram-negative bacterial community than teeth with secondary infections. Moreover, the levels of endotoxins were related to the severity of bone destruction in periapical tissues as well as the development of clinical features in teeth with primary infections.

Clinical and pharmacological management of endodontic flare-up

Knowledge of the causes of and mechanisms behind interappointment pain in endodontics is of utmost importance for the clinician to properly prevent or manage this undesirable condition. The causative factors of interappointment pain encompass mechanical, chemical, and microbial injuries to the pulp or periradicular tissues, which are induced or exacerbated during root canal treatment. This review article underlines the various treatment modalities for relief of pain and swelling in such situations, including premedication, drainage establishment, relief of occlusion, and intracanal and systemic medication.

Diversity of endodontic microbiota revisited

Although fungi, archaea, and viruses contribute to the microbial diversity in endodontic infections, bacteria are the most common micro-organisms occurring in these infections. Datasets from culture and molecular studies, integrated here for the first time, showed that over 460 unique bacterial taxa belonging to 100 genera and 9 phyla have been identified in different types of endodontic infections. The phyla with the highest species richness were Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Diversity varies significantly according to the type of infection. Overall, more taxa have been disclosed by molecular studies than by culture. Many cultivable and as-yet-uncultivated phylotypes have emerged as candidate pathogens based on detection in several studies and/or high prevalence. Now that a comprehensive inventory of the endodontic microbial taxa has been established, future research should focus on the association with different disease conditions, functional roles in the community, and susceptibility to antimicrobial treatment procedures.

Diversity of spirochetes in endodontic infections

The diversity of spirochetes in primary endodontic infections of teeth with chronic apical periodontitis or acute apical abscesses was investigated using 16S rRNA gene clone library analysis. The prevalences of three common cultivable oral Treponema species were also determined using species-specific nested PCR. All detected spirochetes belonged to the genus Treponema. Overall, 28 different taxa were identified from the 431 clones sequenced: 9 cultivable and validly named species, 1 cultivable as-yet-uncharacterized strain, and 18 as-yet-uncultivated phylotypes, 17 of which were novel. The large majority of clones (94%) were from cultivable named species. The numbers of Treponema species/phylotypes per selected positive sample ranged from 2 to 12. Species-specific nested PCR detected T. denticola, T. socranskii, and T. maltophilum in 59 (66%), 33 (37%), and 26 (29%) of the 90 cases of primary endodontic infections, respectively. Clone library analysis revealed diverse Treponema species/phylotypes as part of the microbiota associated with asymptomatic and symptomatic (abscess) endodontic infections. Although several as-yet-uncultivated Treponema phylotypes were disclosed, including novel taxa, cultivable named species were more abundant and frequently detected.

Association of unique, isolated treponemes with bovine digital dermatitis lesions

This study used a PCR-based approach targeting 16S rRNA gene fragments to determine the occurrence and association of the three bovine digital dermatitis (BDD) treponeme phylogroups within lesions found in cattle from the United Kingdom. Examination of 51 BDD lesions collected from infected cattle across the United Kingdom revealed that BDD treponeme group 1 (Treponema medium/Treponema vincentii-like), group 2 (Treponema phagedenis-like), and group 3 (Treponema putidum/Treponema denticola-like) were present in 96.1%, 98%, and 76.5% of BDD lesions, respectively. The three phylogroups were present together in 74.5% of lesions. The PCR assays enabled the isolation of further treponeme strains from previously mixed primary BDD lesion cultures. Here a representative from each of the three distinct treponeme phylogroups was isolated from a single BDD lesion for the first time. These data highlight the extent to which this disease is polytreponemal. Immunohistochemistry and electron microscopy were used to investigate lesional hoof tissues, resulting in treponemes being identified copiously in hair follicles and sebaceous glands, suggesting a potential route of exit and/or entry for these pathogens. This study gives further evidence for the importance of the three treponeme groups in BDD pathogenesis and reiterates the value of molecular genetic approaches for isolating and identifying fastidious anaerobes.

Root canal microbiota of teeth with chronic apical periodontitis

Samples from infected root canals of 43 teeth with chronic apical periodontitis were analyzed for the presence and relative levels of 83 oral bacterial species and/or phylotypes using a reverse-capture checkerboard hybridization assay. Associations between the most frequently detected taxa were also recorded. The most prevalent taxa were Olsenella uli (74%), Eikenella corrodens (63%), Porphyromonas endodontalis (56%), Peptostreptococcus anaerobius (54%), and Bacteroidetes oral clone X083 (51%). When prevalence was considered only for bacteria present at levels >10(5), Bacteroidetes clone X083 was the most frequently isolated bacterium (37%), followed by Parvimonas micra (28%), E. corrodens (23%), and Tannerella forsythia (19%). The number of target taxa per canal was directly proportional to the size of the apical periodontitis lesion, with lesions >10 mm in diameter harboring a mean number of approximately 20 taxa. Several positive associations for the most prevalent taxa were disclosed for the first time and may have important ecological and pathogenic implications. In addition to strengthening the association of several cultivable named species with chronic apical periodontitis, the present findings using a large-scale analysis allowed the inclusion of some newly named species and as-yet-uncultivated phylotypes in the set of candidate pathogens associated with this disease.

Evaluation of the microbiota of primary endodontic infections using checkerboard DNA-DNA hybridization

BACKGROUND/AIMS

The aim of this study was to evaluate the composition of the microbiota of primary endodontic infections in 111 selected cases of single-rooted teeth with necrotic pulp.

METHODS

Samples were collected from the root canals using #15 Hedströen-type files and two sterile paper points, which were introduced 1 mm short of the apical foramen. The presence, levels, and proportions of 40 different bacterial species in each sample were determined using DNA probes and checkerboard DNA-DNA hybridization techniques.

RESULTS

The mean number of species per sample was 22. Enterococcus faecalis (89.3%), Campylobacter gracilis (89.3%), Leptotrichia buccalis (89.3%), Neisseria mucosa (87.5%), Prevotella melaninogenica (86.6%), Fusobacterium nucleatum ssp. vincentii (85.7%), Eubacterium saburreum (75.9%), Streptococcus anginosus (75%), and Veillonella parvula (74.1%) were the most prevalent species. The species found in highest mean counts (over 10(5)) were F. nucleatum ssp. vincentii (13.14 x 10(5)), E. saburreum (5.67 x 10(5)), E. faecalis (5.38 x 10(5)), N. mucosa (4.19 x 10(5)), V. parvula (3.63 x 10(5)), C. gracilis (3.46 x 10(5)), Treponema socranskii (3.34 x 10(5)), Porphyromonas endodontalis (2.96 x 10(5)), Porphyromonas gingivalis (2.85 x 10(5)), Micromonas micros (2.81 x 10(5)), Prevotella nigrescens (2.68 x 10(5)) and Fusobacterium nucleatum ssp. nucleatum (2.64 x 10(5)). Most of these species were also found in high proportions.

CONCLUSIONS

Our results suggest that several bacterial species considered to be oral pathogens seem to be implicated in the etiology of primary endodontic infections.

A big role for the very small--understanding the endodontic microbial flora

Apical periodontitis, an inflammatory process around the apex of a tooth root, is primarily a sequel to microbial infection of the pulp space. The microbial flora is composed of a restricted group of the total oral flora, selected by environmental pressures of anaerobiosis, nutrition and competition with other species and inhabits the root canal as a biofilm of coaggregated communities in an extracellular matrix. The untreated infected canal is generally composed of a polymicrobial mix with approximately equal proportions of Gram-positive and Gram-negative species, dominated by obligate anaerobes. The type of microbial flora in the root-filled tooth with persistent apical periodontitis has very different characteristics. These infections are characterized by one or just a few species, predominantly Gram-positive micro-organisms with an equal distribution of facultative and obligate anaerobes. Enterococcus faecalis has been a conspicuous finding in most studies. Because the primary aetiological problem is infection, endodontic treatment is directed at control and elimination of the root canal flora by working in a sterile way. Based on current knowledge, the best available method for obtaining clean, microbe-free root canals is by instrumentation with antimicrobial irrigation reinforced by an intracanal dressing with calcium hydroxide.

Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis

This study compared the bacterial community profiles of the microbiota associated with acute apical abscesses from Brazilian and USA patients using denaturing gradient gel electrophoresis (DGGE). DNA was extracted from purulent exudate aspirates and part of the 16S rRNA gene was amplified by polymerase chain reaction and separated by DGGE. The resulting banding patterns, which were representative of the bacterial community structures in samples from the two locations, were then compared. Distinct DGGE banding patterns were observed from different samples. Ninety-nine bands with distinct positions in the gels were detected, of which 27 were found only in the USA samples and 13 were exclusive to Brazilian samples. Four of the 59 shared bands showed very discrepant findings with regard to prevalence in the two locations. Cluster analysis of DGGE banding profiles showed a great variability in the bacterial populations associated with teeth with abscesses regardless of the geographical location. Two big clusters, one for each location, were observed. Other clusters contained a mixture of samples from the two locations. The results of the present study demonstrated a great variability in the bacterial community profiles among samples. This indicates that the bacterial communities of abscesses are unique for each individual in terms of diversity. The composition of the microbiota in some samples showed a geography-related pattern. Furthermore, several bands were exclusive for each location and others were shared by the two locations and showed great differences in prevalence.

Searching for Archaea in infections of endodontic origin

Archaea is a highly diverse group of prokaryotes, whose members have been traditionally recognized as extremophiles. Recently, some of these microorganisms have also been found to thrive in nonextreme environments, including the human body. Methanogenic archaea have been detected in samples from subgingival plaque associated with periodontal disease and a pathogenetic role is suspected. The purpose of this study was to survey samples taken from different types of endodontic infections for the presence of archaea. Samples were taken from untreated and treated root canals associated with asymptomatic chronic periradicular lesions as well as from cases diagnosed as acute periradicular abscesses. Overall, 96 samples were obtained. DNA from samples was extracted by using two different protocols and used as template for polymerase chain reaction amplification using oligonucleotide universal primers for the domains Archaea or Bacteria. Samples were also checked for the presence of spirochetes by making use of a group-specific primer. While bacteria were present in all samples, no case yielded archaeal DNA. Spirochetes occurred in a high number of cases. Our findings suggested that members of the Archaea domain are not members of the microbiota present in different types of endodontic infections and thereby may not be implicated in the etiology of apical periodontitis.

Occurrence of two newly named oral treponemes -Treponema parvum and Treponema putidum- in primary endodontic infections

BACKGROUND/AIMS

Recent evidence from molecular genetic studies has revealed that oral Treponema species are involved in infections of endodontic origin. This study assessed the occurrence of two newly named oral treponemes - Treponema parvum and Treponema putidum - in primary endodontic infections using a culture-independent identification technique.

METHODS

Genomic DNA was isolated directly from clinical samples, and a 16S rRNA gene-based nested polymerase chain reaction (PCR) assay was used to determine the presence of T. parvum and T. putidum. Species-specific primer pairs were developed by aligning closely related 16S rRNA gene sequences. The specificity for each primer pair was validated by running PCR against a panel of oral bacteria and by sequence analysis of PCR products from positive clinical samples.

RESULTS

T. parvum was detected in 52% of the root canals associated with chronic apical periodontitis, in 20% of the cases diagnosed as acute apical periodontitis, and in no abscessed case. In general, T. parvum was detected in 26% of the samples from primary endodontic infections. T. putidum was found in only one case of acute apical periodontitis (2% of the total number of cases investigated).

CONCLUSIONS

The devised nested PCR protocol was able to identify both T. parvum and T. putidum directly in clinical samples and demonstrated that these two treponemes can take part in endodontic infections.

Uncultivated phylotypes and newly named species associated with primary and persistent endodontic infections

Endodontic infections have been traditionally studied by culture methods, but recent reports showing that over 50% of the oral microbiota is still uncultivable (B. J. Paster et al., J. Bacteriol. 183:3770-3783, 2001) raise the possibility that many endodontic pathogens remain unknown. This study intended to investigate the prevalence of several uncultivated oral phylotypes, as well as newly named species in primary or persistent endodontic infections associated with chronic periradicular diseases. Samples were taken from the root canals of 21 untreated teeth and 22 root-filled teeth, all of them with radiographic evidence of periradicular bone destruction. Genomic DNA was isolated directly from each sample, and 16S rRNA gene-based nested or heminested PCR assays were used to determine the presence of 13 species or phylotypes of bacteria. Species-specific primers had already been validated in the literature or were developed by aligning closely related 16S rRNA gene sequences. Species specificity for each primer pair was confirmed by running PCRs against a panel of several oral bacteria and by sequencing DNA from representative positive samples. All species or phylotypes were detected in at least one case of primary infections. The most prevalent species or phylotypes found in primary infections were Dialister invisus (81%), Synergistes oral clone BA121 (33%), and Olsenella uli (33%). Of the target bacteria, only these three species were detected in persistent infections. Detection of uncultivated phylotypes and newly named species in infected root canals suggests that there are previously unrecognized bacteria that may play a role in the pathogenesis of periradicular diseases.

Exploiting Molecular Methods to Explore Endodontic Infections: Part 2—Redefining the Endodontic Microbiota

The second part of this review discusses the application of molecular methods in endodontic microbiology research for a comprehensive characterization of the microbiota associated with different types of endodontic infections. Despite their recent introduction in endodontic research, molecular methods have already given a significant contribution to the understanding of endodontic infections and the future holds the perspective of a still better refinement of the knowledge about these infections. Molecular methods have revealed a higher complexity of the endodontic microbiota than previously reported by cultivation approaches. In addition to detecting some cultivable species in increased prevalence, molecular methods have also expanded the list of putative endodontic pathogens by inclusion of some fastidious bacterial species or even uncultivated bacteria that have never been previously found in endodontic infections.

Differences in prevalence of selected bacterial species in primary endodontic infections from two distinct geographic locations

OBJECTIVE

This study intended to compare the prevalence of 7 putative endodontic pathogens in samples of primary endodontic infections taken from patients of 2 distant geographic locations.

STUDY DESIGN

Samples from infected root canals associated with asymptomatic periradicular lesions or from pus aspirated from acute periradicular abscesses were collected from patients in Rio de Janeiro, Brazil, and Seoul, South Korea. South Korean samples were frozen and delivered to Brazil, where all steps in the molecular analysis were performed. DNA was extracted and a species-specific nested polymerase chain reaction assay was used to detect 7 target bacterial species.

RESULTS

The most prevalent species detected in Brazilian samples were Porphyromonas endodontalis (79% of the cases) , Treponema denticola (79%), and Dialister pneumosintes (76%). The most prevalent species found in South Korean samples were Fusobacterium nucleatum (38% of the cases) , Tannerella forsythia (26%), and Treponema maltophilum (24%). Overall, P endodontalis, D pneumosintes, Filifactor alocis, T denticola, and T forsythia were significantly more detected in Brazilian samples than in South Korean samples ( P < .05).

CONCLUSIONS

Findings indicated that the prevalence of some species in infections of endodontic origin may significantly differ from one geographic location to another.

Treponema species associated with abscesses of endodontic origin

Spirochetes have been frequently observed in abscesses of endodontic origin, but they have rarely been identified. This study sought to investigate the prevalence of eight oral treponemes in acute periradicular abscesses using a species-specific nested polymerase chain reaction assay. Purulent exudate was collected by aspiration from 19 cases diagnosed as acute periradicular abscesses and DNA extracted from the samples was initially amplified using universal 16S rDNA primers. A second round of amplification used the first polymerase chain reaction products to detect a specific fragment of the 16S rDNA of each Treponema species. The species-specific nPCR assay used in this study allowed the detection of Treponema denticola in 79%(15 of 19), Treponema socranskii in 26%(5 of 19), Treponema pectinovorum in 21% (4 of 19), Treponema amylovorum in 16% (3 of 19), and Treponema medium in 5% (1 of 19) of the cases. Spirochetal DNA was found in 89% of the cases (17 of 19). The number of Treponema species per case ranged from 1 to 3 (mean, 1.5). Treponema vincentii, Treponema lecithinolyticum and Treponema maltophilum were not detected in any pus sample. The present data lend support to the assertion that Treponema species, particularly T. denticola and T. socranskii, may be involved in the pathogenesis of acute periradicular abscesses.

Geographical Differences in Bacteria Detected in Endodontic Infections Using Polymerase Chain Reaction

The polymerase chain reaction (PCR) is an innovative nucleic acid-based assay that has the highest sensitivity of any microbiological technique for the detection of bacteria. The purpose of this study was to use PCR to detect the presence of specific species of bacteria in samples collected from two geographical locations. Microbial samples from abscesses of endodontic origin were collected from patients in Portland, Oregon, and Rio de Janeiro, Brazil. PCRs with species-specific oligonucleotide primers for the 16S ribosomal RNA gene were used for detection of the bacteria after DNA extraction from each clinical sample. Statistical analysis revealed that there was a significant difference in detection of the bacteria between the two geographical locations for Prevotella intermedia, Prevotella nigrescens, Prevotella tannerae, Fusobacterium nucleatum, and Porphyromonas gingivalis, but not for Porphyromonas endodontalis, Fusobacterium necrophorum, and Enterococcus faecalis. These results suggest that differences in bacteria detected or cultured in studies can be associated with geographical location.

Taxonomic changes of bacteria associated with endodontic infections

There have been major recent reorganizations among bacterial taxa as a result of phylogenetic taxonomic approaches. As a consequence, old species have been renamed and novel species have been proposed. The introduction of molecular technology for microbial identification has also allowed the detection of microbial taxa never previously found in endodontic infections. Therefore, the list of putative endodontic pathogens is frequently changing and expanding. The purpose of this review is twofold: to cover the taxonomic changes that the major putative endodontic pathogens have undergone in the recent years and to compile data from studies regarding the detection of known or novel bacterial species that had been only recently reported to occur in endodontic infections.

PCR methodology as a valuable tool for identification of endodontic pathogens

OBJECTIVES

This paper reviews the principles of polymerase chain reaction (PCR) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.

DATA SOURCES

Studies published in the medical, dental and biological literature.

STUDY SELECTION

Evaluation of published epidemiological studies examining the endodontic microbiota through PCR methodology.

CONCLUSIONS

PCR technology has enabled the detection of bacterial species that are difficult or even impossible to culture as well as cultivable bacterial strains showing a phenotypically divergent or convergent behaviour. Moreover, PCR is more rapid, much more sensitive, and more accurate when compared with culture. Its use in endodontics to investigate the microbiota associated with infected root canals has expanded the knowledge on the bacteria involved in the pathogenesis of periradicular diseases. For instance, Tannerella forsythensis (formerly Bacteroides forsythus), Treponema denticola, other Treponema species, Dialister pneumosintes, and Prevotella tannerae were detected in infected root canals for the first time and in high prevalence when using PCR analysis. The diversity of endodontic microbiota has been demonstrated by studies using PCR amplification, cloning and sequencing of the PCR products. Moreover, other fastidious bacterial species, such as Porphyromonas endodontalis, Porphyromonas gingivalis and some Eubacterium spp., have been reported in endodontic infections at a higher prevalence than those reported by culture procedures.

PCR-based identification of Treponema maltophilum, T amylovorum, T medium, and T lecithinolyticum in primary root canal infections

OBJECTIVE

Molecular genetic methods have significantly contributed to the knowledge about the microbiota associated with infected root canals. Albeit spirochetes have been commonly observed in primary root canal infections, only recently they have been identified. The purpose of the present study was to investigate the occurrence of four treponemes-Treponema maltophilum, Treponema lecithinolyticum, Treponema amylovorum, and Treponema medium-in cases of primary endodontic infections associated with different forms of periradicular diseases through a 16S rDNA-based nested PCR assay.

DESIGN

Samples were taken from thirty-one infected root canals associated with either asymptomatic or symptomatic apical periodontitis. DNA extracted from the samples was initially amplified using universal 16S rDNA primers, followed by a second round of amplification using the first PCR products to detect a specific fragment of the 16S rDNA of each target Treponema species.

RESULTS

All cases were positive for the universal bacterial primers, indicating that samples contained bacterial DNA. Of the four target species, T. maltophilum was the most prevalent, being detected in 39% of the cases (33% of the asymptomatic cases and 50% of the symptomatic cases). T. lecithinolyticum was the next more prevalent among the species tested, being found in 26% of the samples (33% of asymptomatic cases and 10% of the symptomatic cases). T. amylovorum was found in 7% of the cases (5% of the asymptomatic cases and 10% of the symptomatic cases), while T. medium was in 13% of the cases (14% of the asymptomatic cases and 10% of the symptomatic cases). None of the species tested was significantly associated with clinical symptoms.

CONCLUSIONS

This was possibly the hitherto first study to report the occurrence of T. lecithinolyticum, T. amylovorum, and T. medium in infections of endodontic origin. Overall, findings suggested that these oral treponemes, particularly T. maltophilum and T. lecithinolyticum, can be involved in the pathogenesis of periradicular diseases.