Checkerboard DNA-DNA hybridization analysis of endodontic infections

A novel experimental model to investigate fungal involvement shows expression of Dectin-1 in periapical lesion pathogenesis

BACKGROUND

Candida albicans is linked to persistent endodontic lesions. However, the recognition receptor that identifies it is not explored previously.

OBJECTIVES

The aim of this study was to (1) establish a zymosan-induced model of apical periodontitis in mouse, (2) observe the expression of Dectin-1 and its possible relationship with toll-like receptor (TLR) 2 and (3) observe relationship between Osteopontin (OPN) and inflammatory cytokines.

METHODS

A total of 138 Naval Medical Research Institute (NMRI) mice were randomly divided into; Experimental Group n = 69 and Zymosan Group n = 69. Periapical periodontitis was developed in right maxillary molar. The animals were sacrificed at 7, 21 and 42 days. Bone blocks containing the mesial root (n = 15 for qRT-PCR, n = 45 for enzyme-linked immune sorbent assay (ELISA)) were collected for mRNA expression and ELISA. While whole maxilla (n = 3 from each time interval) were used for histology and immunohistochemical analysis. One way analysis of variance (ANOVA) and Tuckey's posthoc was used for statistical analysis at p ≤ .05.

RESULTS

TLR-2, Dectin-1 and TLR4-positive cells was detected at all time intervals in both groups. A strong positive correlation was observed between TLR-2 and Dectin-1 in both lesions (regular r = .680, p = .015, zymosan (r = .861, p < .001)). A significant correlation was found between OPN and tumour necrosis factor-alpha (TNF-α) in zymosan lesion (r = .827, p = .001).

CONCLUSIONS

Immune cells of inflamed periapical tissue expressed Dectin-1 receptor in response to the microbial challenge from infected root canals and showed positive correlation with TLR-2 and OPN suggesting a possible receptor collaboration mediated by OPN. The expression of OPN and TNF-α showed positive correlation in response to fungal antigen, indicating a possible relationship.

Centric versus eccentric engine-driven endodontic instrument design for microbial load reduction-A systematic review and meta-analysis of randomised clinical trials

This systematic review assessed the clinical influence of centric and eccentric engine-driven instrument design for reduction in microbial load in infected root canal system. The literature search was conducted in electronic databases (PubMed, Cochrane Library, Scopus, Lilacs and Google Scholar) and grey literature till June 2022. The search strategy followed the PRISMA 2020 guidelines. Qualitative and quantitative synthesis was conducted based on the guidelines of the Cochrane Handbook. The risk of bias was assessed using the revised Cochrane criteria and quality of evidence was conducted using the Grading of Recommendation Assessment, Development and Evaluation tool. Out of 28 papers, only five papers met the inclusion criteria of this review. Studies showed reduction in microbial load after instrumentation using centric or eccentric instruments with no statistically significant difference in the meta-analysis. In conclusion, there is low-grade evidence suggesting that microbial reduction is similar using centric and eccentric instruments.

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.

The impact of an enhanced infection control protocol on the microbial community profile in molar root canal treatment-an in vivo NGS molecular study

INTRODUCTION

Recent findings demonstrated that one-year CBCT-based outcomes of molar root canal treatment were improved through an Enhanced infection protocol (EnP), when compared to a current best-practice standard infection control protocol (StP). The EnP comprised measures to reduce iatrogenic contamination from direct and indirect contact surfaces, including the replacement of the rubber dams, gloves, files, all instruments, and surface barriers before root canal obturation. The aim of this study was to investigate the effect of such an enhanced infection control protocol on resident microbiome present after chemomechanical instrumentation and the protocol ability in reducing iatrogenic contamination in molar teeth during root canal treatment.

METHODS

Molar teeth were block-randomized to receive either treatment under EnP or StP. To compare the differential effect of the protocol on the identity of bacteria present, one hundred and fifty, matched DNA extracts from 75 molar teeth samples (StP, n=39; EnP, n=36), were evaluated. Samples were taken before (S1) and after (S2) chemomechanical preparation and were subjected to next-generation sequencing of the V3-V4 region of the 16S rRNA gene, prior to bioinformatical identification using the HOMD oral microbiome database and downstream taxonomic processing, providing measures of richness and diversity of bacteria and significant bacterial taxa during chemomechanical instrumentation and the effect of the two treatment groups.

RESULTS

88 microbial taxa were significantly more abundant in StP S2 samples, including endodontically relevant contaminants taxa as Actinomyces, Cutibacterium, and Haemophilus. The S2 samples demonstrated fewer residual bacterial species in the EnP group, with 26.8 observed species compared to 38.3 in the StP. Reduced diversity and richness measures were noted in the EnP pre-obturation samples compared to the StP in OTU, Chao1 and ACE indices (p≤0.05). Differential microbial identities between S1 and S2 samples and protocols demonstrated that the previously observed increased effectiveness of the EnP protocol was likely to prevent recontamination or de novo contamination of the root canal space during treatment.

CONCLUSIONS

The implemented enhanced infection control protocol resulted in a specific reduction of microbial taxa often associated with recontamination or iatrogenic contamination, suggesting the basis for improved infection control measures during root canal treatment.

The antibacterial activity of mineral trioxide aggregate containing calcium fluoride

Background/purpose

Because complete microbial elimination of the infected root canal system is nearly impossible to achieve, the use of root canal fillings with antibacterial effects may help to minimize intracanal infections. Our previous study, MTA modified by CaF₂ addition, improved the biocompatibility and mineralization potential of human dental pulp cells without adverse effect on the physical properties. In this study, the antibacterial effect of MTA after CaF₂ addition was evaluated for use as a root canal sealer. The objective of this study was to evaluate the antibacterial activity of MTA after the addition of CaF₂.

Materials and methods

The antibacterial activities of MTA and MTA–CaF₂ mixture against Enterococcus faecalis (E. faecalis), Porphyromonas endodontalis (P. endodontalis), and Porphyromonas gingivalis (P. gingivalis) were investigated with MTA-CaF₂ powder and eluates. The bacterial growth was measured by optical density using a spectrophotometer and the bacterial colony counting.

Results

MTA inhibited the growth of E. faecalis, P. endodontalis, and P. gingivalis, and the addition of CaF₂ improved this antibacterial effect in a concentration dependent manner (p < 0.05). E. faecalis was more resistant to MTA-CaF₂ than the other groups of bacteria.

Conclusion

The addition of more than 5% CaF₂ to MTA can increase the antibacterial activity.

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.

A qualitative and semiquantitative SEM study of the morphology of the biofilm on root surfaces of human teeth with endodontic-periodontal lesions

Over the last decades, scanning electron microscopy (SEM) proved to be invaluable for ultrastructural investigation, allowing imaging of the overall appearance and/or specific features of oral biofilms, e.g., microbial colonies and individual cells, glycocalyx, the presence of inorganic products. The aim of this study was the observation and evaluation of the morphology of the biofilm of endodontic-periodontal lesions (EPL) with a modified protocol involving a simplified histologic sample preparation and a low-vacuum SEM examination method. Twenty-one teeth with endodontic-periodontal involvement, extracted for periodontal reasons, were carefully washed with saline, underwent fixation in modified Karnovsky solution and were dehydrated in alcohol series. Samples were examined under low-vacuum SEM. Radicular surfaces were evaluated qualitatively and semiquantitatively for several characteristics, including the presence of bacterial types, the biofilm morphology and the content of root resorptions. Radicular surfaces were divided in four conventional zones Surfaces were evaluated for several characteristics: Presence of bacterial types, biofilm morphology, presence of root resorptions. High-quality images, relevant for endodontic-periodontal biofilms were collected. Continuous, established biofilm was found on all examined surfaces, its detection varying from 19% of the samples on the wall of cemental cone to 52.3% on the radicular surface of the periodontal pocket. Observed microorganisms included cocci, rods an filaments. Spirils and motile bacteria were only accidentally found. SEM investigation of surfaces involved in EPL revealed less surfaces covered by mature biofilm (in only 28.5% of the samples in the ‘transition zone’), especially rods and filaments associated with cemental resorptions and calculus. Biofilm elements were better represented in periodontal pockets than in other zones of EPL (detected in up to 81% of the samples). A strong correlation between mature biofilm and the presence of cocci appears on all investigated zones (P<0.01). Microbiota appeared to be morphologically similar in apical and periodontal areas, especially in old EPL.

Does Calcium Hydroxide Reduce Endotoxins in Infected Root Canals? Systematic Review and Meta-analysis

INTRODUCTION

The purpose of this study was to evaluate the potential of endotoxin reduction by comparing the number of lipopolysaccharides (LPSs) before and after the use of calcium hydroxide (Ca[OH]₂) as intracanal medication (ICM).

METHODS

Searches were performed up to June 2020. Clinical and experimental studies comparing the amount of LPSs before and after the use of Ca(OH)₂ as ICM in infected root canals were included. Risks of bias assessment and data extraction were performed. Meta-analysis was conducted by subgrouping according to Ca(OH)₂, the presence of an antimicrobial substance (AS), irrigant solution during chemomechanical preparation (CMP), and the incidence of LPS reduction. The certainty of evidence was determined by the Grading of Recommendations Assessment, Development and Evaluation approach.

RESULTS

Nine studies were included in the qualitative synthesis and 7 in the meta-analysis. Three articles had low risk of bias (RB), 1 had moderate RB, 2 had high RB, and 3 "some concerns." Overall, Ca(OH)₂, with or without AS, reduced mean LPSs before CMP (standardized mean difference [SMD] = -1.087 [confidence interval {CI}, -1.453 to -0.721], P < .001, I² = 58.7%) and after CMP (SMD = -0.919 [CI, -1.156 to -0.682], P < .001, I² = 24.7%). Considering the irrigant solutions, the overall results showed a reduction before (SMD = -1.053 [CI, -1.311 to -0.795], P < .001, I² = 58.7%) and after CMP (SMD = -0.938 [CI, -1.147 to -0.729], P < .001, I² = 24,6%). Analyses presented very low certainty of evidence. The incidence of LPS reduction was 98.9% and 61.7% for Ca(OH)₂ with and without AS, respectively.

CONCLUSIONS

Ca(OH)₂ reduces endotoxin levels when used as ICM but is unable to eliminate LPSs completely independent of the irrigating solution used with very low certainty of evidence.

Identification of microorganisms in irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings

OBJECTIVES

The aim of this study was to evaluate the composition of microbiota of irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings by performing cultures and 16s rDNA sequencing in Iranian patients.

MATERIAL AND METHODS

In this prospective cross-sectional study, samples were collected from 41 root canals for 4 main groups of patients. Bacterial identification was performed by the polymerase chain reaction (PCR) and 16s rDNA sequencing of aerobic and anaerobic cultivable colonies taken from patients' culture plates. Additionally, the presence of 13 bacterial species and 3 nonbacterial species was also explored using PCR and species-specific primers.

RESULTS

Sixteen microbial species, 1 fungus (Candida albicans), and 1 virus (Herpes simplex virus) were discovered and isolated. Species with the highest prevalence were Dialister invisus (68.3%), Porphyromonas gingivalis (58.8%), Streptococcus salivarius (58.5%), and Treponema denticola (56.1%). Lysinibacillus fusiformis (19.1%) was detected in the root canals for the first time. Candida albicans was seen in 11 cases (26.8%). Herpes simplex virus (HSV) was seen in 4 patients (9.8%).

CONCLUSIONS

Our results suggest that Gram-negative anaerobic oral bacteria are the majority of the microbes in primary endodontic infections. Various combinations of bacterial species were related to different clinical and radiographic conditions. Lysinibacillus fusiformis was detected for the first time in primary endodontic infections.

CLINICAL RELEVANCE

The results of this investigation might help clinicians choose to identify suspected endodontic pathogens in the etiology of each form of pulpal and periradicular diseases to determine the best therapeutic measures.

Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity

The composition of the oral microbiome in healthy individuals is complex and dynamic, and depends on many factors, such as anatomical location in the oral cavity, diet, oral hygiene habits or host immune responses. It is estimated at present that worldwide about 2 billion people suffer from diseases of the oral cavity, mainly periodontal disease and dental caries. Importantly, the oral microflora involved in local infections may spread and cause systemic, even life-threatening infections. In search for etiological agents of infections in dentistry, traditional approaches are not sufficient, as about 50% of oral bacteria are not cultivable. Instead, metagenomic analyses are particularly useful for studies of the complex oral microbiome - both in healthy individuals, and in patients with oral and dental diseases. In this paper we review the current and future applications of metagenomic studies in evaluation of both the composition of the oral microbiome as well as its potential pathogenic role in infections in dentistry.

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.

Studying the human oral microbiome: challenges and the evolution of solutions

Since the pioneering work of van Leeuwenhoek in 1684, subsequently built upon by other renowned microbiologists Robert Koch, Willoughby Miller and GV Black, oral microbiology has developed innovative techniques to study the oral microflora (now termed the 'oral microbiome'). The advent of molecular techniques such as DNA-DNA hybridization, polymerase chain reaction and DNA sequencing has created an array of opportunities to construct a comprehensive picture of the diversity and composition of the oral microbiome. Approximately 700 oral bacterial species have been identified, of which 50% have yet to be cultivated, and some of these are known only by their signature DNA sequences. The synergism of ever-evolving culture-based and state-of-the-art culture-independent molecular techniques has facilitated in-depth understanding of the dynamics, acquisition and transfer of oral bacteria, along with their role in oral and general health and disease. Further research is needed to not only analyse but also to make sense of the ever-increasing volumes of data which these molecular techniques (especially high-throughput DNA sequencing) are generating, as well as why particular bacteria are present and what they are 'actually doing' there. This review presents a comprehensive literature search of oral microbiology-related methods currently used to study the oral microbiome.

On the dynamics of root canal infections-what we understand and what we don't

Infections of the root canal space and their sequelae can be extremely painful and potentially dangerous, yet they do not necessarily have to be. Chronic, asymptomatic inflammatory lesions around the apex of a tooth with a necrotic dental pulp or an insufficient root canal treatment can develop unnoticed by the patient, and remain so for years. The course of disease is modulated by both the virulence of the microbiota established in the root canal space and the capacity of the immune system to curb the infection. To both ends, highly convincing investigations to help us understand when and why the tissues around an endodontically involved tooth become acutely inflamed are missing. We will discuss how recent advances in molecular identification of microorganisms have altered our understanding of root canal infections, and which information is currently missing to link clinical experience with observations from experimental research.

Short-chain Fatty Acids in Infected Root Canals of Teeth with Apical Periodontitis before and after Treatment

INTRODUCTION

Short-chain fatty acids (SCFAs) are bacterial metabolic end products that may function as virulence factors. This study evaluated the occurrence of SCFAs in infected root canals before and after treatment.

METHODS

Samples were taken from root canals of teeth with apical periodontitis before (S1) and after (S2) chemomechanical preparation with either NaOCl or chlorhexidine as the irrigant and then after interappointment medication with calcium hydroxide (S3). High-performance liquid chromatography was used for detection of SCFAs. Selected bacterial taxa that are recognized producers of the target SCFAs were identified by real-time polymerase chain reaction.

RESULTS

Butyric acid was the most common fatty acid in S1, followed by propionic acid. Both molecules were also found in S2 and S3 from both NaOCl and chlorhexidine groups. Lactic acid was not present in detectable levels in S1, but it occurred in 1 postinstrumentation sample and in 9 samples taken after calcium hydroxide medication. Of the target taxa, Fusobacterium nucleatum was the most prevalent in S1 (76%), followed by members of the Actinobacteria phylum (71%), Streptococcus species (59%), and Parvimonas micra (53%). Gram-positive taxa, especially streptococci, were the most prevalent bacteria in S2 and S3. SCFA detection was matched with the respective potential producer species in most cases.

CONCLUSIONS

This first report of SCFAs in infected root canals suggests that these molecules may play a role in the pathogenesis of apical periodontitis. Significance of persistence of SCFAs after treatment and its effects on the long-term outcome await elucidation.

Antimicrobial peptide-based treatment for endodontic infections--biotechnological innovation in endodontics

The presence/persistence of microorganisms in the pulp and periapical area corresponds to the maintenance of an exacerbated immune response that leads to the start of periradicular bone resorption and its perpetuation. In endodontic treatment, the available intracanal medications do not have all the desirable properties in the context of endodontic infection and apical periodontitis; they need to include not only strong antimicrobial performance but also an immunomodulatory and reparative activity, without host damage. In addition, there are various levels of resistance to root canal medications. Thus, antimicrobial agents that effectively eliminate resistant species in root canals could potentially improve endodontic treatment. In the emergence of new therapies, an increasing number of studies on antimicrobial peptides (AMPs) have been seen over the past few years. AMPs are defense biomolecules produced in response to infection, and they have a wide spectrum of action against many oral microorganisms. There are some studies that correlate peptides and oral infections, including oral peptides, neuropeptides, and bacterial, fish, bovine and synthetic peptides. So far, there are around 120 published studies correlating endodontic microbiota with AMPs but, according to our knowledge, there are no registered patents in the American patent database. There are a considerable number of AMPs that exhibit excellent antimicrobial activity against endodontic microbiota at a small inhibitory concentration and modulate an exacerbated immune response, down-regulating bone resorption. All these reasons indicate the antimicrobial peptide-based endodontic treatment as an emerging and promising option.

The oral microbiome diversity and its relation to human diseases

As one of the most clinically relevant human habitats, the human mouth is colonized by a set of microorganisms, including bacteria, archaea, fungi, and viruses. Increasing evidence has supported that these microbiota contribute to the two commonest oral diseases of man (dental caries and periodontal diseases), presenting significant risk factors to human health conditions, such as tumor, diabetes mellitus, cardiovascular diseases, bacteremia, preterm birth, and low birth weight in infants. It is widely accepted that oral microorganisms cause diseases mainly by a synergistic or cooperative way, and the interspecies interactions within the oral community play a crucial role in determining whether oral microbiota elicit diseases or not. Since a comprehensive understanding of the complex interspecies interactions within a community needs the knowledge of its endogenous residents, a plenty of research have been carried out to explore the oral microbial diversity. In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis

Despite increasing knowledge on phylogenetic composition of the human microbiome, our understanding of the in situ activities of the organisms in the community and their interactions with each other and with the environment remains limited. Characterizing gene expression profiles of the human microbiome is essential for linking the role of different members of the bacterial communities in health and disease. The oral microbiome is one of the most complex microbial communities in the human body and under certain circumstances, not completely understood, the healthy microbial community undergoes a transformation toward a pathogenic state that gives rise to periodontitis, a polymicrobial inflammatory disease. We report here the in situ genome-wide transcriptome of the subgingival microbiome in six periodontally healthy individuals and seven individuals with periodontitis. The overall picture of metabolic activities showed that iron acquisition, lipopolysaccharide synthesis and flagellar synthesis were major activities defining disease. Unexpectedly, the vast majority of virulence factors upregulated in subjects with periodontitis came from organisms that are not considered major periodontal pathogens. One of the organisms whose gene expression profile was characterized was the uncultured candidate division TM7, showing an upregulation of putative virulence factors in the diseased community. These data enhance understanding of the core activities that are characteristic of periodontal disease as well as the role that individual organisms in the subgingival community play in periodontitis.

Pi30 DNA Probe May Be Useful for the Identification ofPrevotella intermediaat the Species or Strain Level

Recently, we introduced a new method for the rapid screening of bacterial species-or subspecies-specific DNA probes, named the "inverted dot blot hybridization screening method." This method has subsequently been then applied to develop species-or strain-specific DNA probes for Prevotella intermedia and Prevotella nigrescens. In a previous study, the inverted dot blot hybridization data showed that a probe, Pi30, was specific for P. intermedia. In this study, the DNA probe Pi30 was evaluated by Southern blot analysis to determine if it could distinguish P. intermedia from P. nigrescens. The data showed that the probe Pi30 reacted with the genomic DNAs from the reference strains and clinical isolates of both P. intermedia and P. nigrescens, but the size of the signal bands was different. In addition, the probe Pi30 reacted with a 1.4 kbp fragment from the genomic DNAs digested with Pst I of the P. intermedia strains but not with any fragments of P. nigrescens strains. The result indicates that the probe Pi30 could be useful for the identification of P. intermedia by restriction fragment length polymorphism (RFLP) at the species or strain level.

Microbiology and treatment of acute apical abscesses

Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease.

Comparing the bacterial diversity of acute and chronic dental root canal infections

This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic) or chronic (asymptomatic) apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs) (at 3% divergence) belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%), Fusobacteria (17%) and Bacteroidetes (13%), while in chronic infections the dominant were Firmicutes (59%), Bacteroidetes (14%) and Actinobacteria (10%). Members of Fusobacteria were much more prevalent in acute (89%) than in chronic cases (50%). The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165) of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic). This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections.

Real-time polymerase chain reaction of "red complex" (Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola) in periradicular abscesses

OBJECTIVE

The red complex bacteria (Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola) have been implicated, either singly or in combination, in the development of various forms of periodontal diseases. The aim of this study was to investigate the presence of "red complex" in acute periradicular abscesses by real-time polymerase chain reaction (PCR) method.

STUDY DESIGN

Microbial samples were collected by aspiration from 32 cases diagnosed as acute periradicular abscess. DNA was extracted from the samples by using a QIAamp DNA mini-kit and analyzed with real-time PCR.

RESULTS

At least 1 member of the red complex was found in 84% of the cases. In general T. denticola, P. gingivalis, and T. forsythia were detected in 65.6%, 43.7%, and 40.6% of the cases, respectively. Red complex was detected in 15.6% of samples taken from acute periradicular abscesses.

CONCLUSIONS

Our findings suggest that "red complex" can participate in the pathogenesis of acute periradicular abscesses.

Microbiota of deciduous endodontic infections analysed by MDA and Checkerboard DNA-DNA hybridization

AIMS

To evaluate the microbiota of endodontic infections in deciduous teeth by Checkerboard DNA-DNA hybridization after uniform amplification of DNA in samples by multiple displacement amplification (MDA).

METHODOLOGY

Forty samples from the root canal system of deciduous teeth exhibiting pulp necrosis with or without radiographically detectable periradicular/interradicular bone resorption were collected and 32 were analysed, with three individuals contributing two samples; these were MDA-amplified and analysed by Checkerboard DNA-DNA hybridization for levels of 83 bacterial taxa. Two outcome measures were used: the percentage of teeth colonized by each species and the mean proportion of each bacterial taxon present across all samples.

RESULTS

The mean amount of DNA in the samples prior to amplification was 5.2 (±4.7) ng and 6.1 (±2.3) μg after MDA. The mean number of species detected per sample was 19 (±4) (range: 3-66) to the nearest whole number. The most prevalent taxa were Prevotella intermedia (96.9%), Neisseria mucosa (65.6%), Prevotella nigrescens (56.2%) and Tannerella forsythia (56.2%). Aggregatibacter (Haemophilus) aphrophilus and Helicobacter pylori were not detected. P. intermedia (10%), Prevotella tannerae (7%) and Prevotella nigrescens (4.3%) presented the highest mean proportions of the target species averaged across the positive samples.

CONCLUSION

Root canals of infected deciduous teeth had a diverse bacterial population. Prevotella sp. were commonly found with P. intermedia, Prevotella tannerae and Prevotella nigrescens amongst the most prominent species detected.

Prediction of plausible bacterial composition based on terminal restriction fragment length polymorphisms using a Monte Carlo method

We have developed a new approach for the estimation of bacterial proportional compositions in microbiota based on terminal restriction length polymorphism (T-RFLP) data and a Monte Carlo algorithm. This program estimates proportional compositions by minimizing distances between peak values and the relative abundance of each group, containing several species, estimated from peak areas of capillary electrophoresis for T-RFLP analysis. Oral bacteria in 36 saliva samples obtained from three individuals were analyzed using the program. Upon comparison, the estimated proportional composition obtained from one of the samples matched that from a clone library. Additionally, comparisons among the bacterial proportional compositions of saliva samples obtained from three individuals four times per day for 3 days revealed that the types of microbiota present in each individual did not change within each 24-h time period and were distinguishable from those in other individuals.

Distribution of Porphyromonas gingivalis fimA genotypes in primary endodontic infections

OBJECTIVE

Long fimbriae (FimA) are important virulence factors of Porphyromonas gingivalis. Based on the diversity of the fimA gene, this species is classified into 6 genotypes. This study surveyed samples from primary endodontic infections for the presence of these P. gingivalis fimA variants.

STUDY DESIGN

Genomic DNA isolated from samples taken from 25 root canals of teeth with chronic apical periodontitis and 25 aspirates from acute apical abscess was used as template in polymerase chain reaction (PCR) assays directed toward the detection of the different P. gingivalis fimA genotypes.

RESULTS

Porphyromonas gingivalis was detected by a 16S rRNA gene-based PCR in 36% of the total number of cases sampled (44% of chronic apical periodontitis and 28% of abscess aspirates). In cases of chronic apical periodontitis, P. gingivalis variant type IV was the most prevalent (24%), followed by types I (20%), II (16%), and III (8%). In acute abscess samples, variant type II was the most prevalent (12%), followed by types III and IV (8% of each) and type I (4%). Combinations of up to 3 different genotypes were detected in a few cases. No single fimA genotype variant or combination thereof was significantly associated with symptoms. Overall, fimA types IV (16%), II (14%), and I (12%) were the most prevalent.

CONCLUSIONS

Findings demonstrated that different P. gingivalis fimA genotypes can be present in primary endodontic infections.

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.

Distinctive features of the microbiota associated with different forms of apical periodontitis

Microorganisms infecting the dental root canal system play an unequivocal role as causative agents of apical periodontitis. Although fungi, archaea, and viruses have been found in association with some forms of apical periodontitis, bacteria are the main microbial etiologic agents of this disease. Bacteria colonizing the root canal are usually organized in communities similar to biofilm structures. Culture and molecular biology technologies have demonstrated that the endodontic bacterial communities vary in species richness and abundance depending on the different types of infection and different forms of apical periodontitis. This review paper highlights the distinctive features of the endodontic microbiota associated with diverse clinical conditions.

MTA preparations from different origins may vary in their antimicrobial activity

OBJECTIVE

The antimicrobial effects of 4 mineral trioxide aggregate (MTA) preparations, 2 white-colored (WMTA-1, WMTA-2) and 2 gray-colored (GMTA-1, GMTA-2), against C. albicans and E. faecalis were assessed in vitro.

METHODOLOGY

Minimal inhibitory concentration (MIC) for each preparation was determined using the tube dilution test and Sabouraud agar media for C. albicans and brain heart infusion media for E. faecalis. Broth tubes were prepared and divided into experimental and control groups. Aliquots of each of the tested microorganisms were taken from a stock culture and added to each experimental and positive control group. All groups were incubated at 37 degrees C and evaluated for turbidity at 24-, 48-, and 72-hour time periods. Samples of 0.1 mL from each of the experimental and control tubes were subcultured on agar or brain heart infusion plates to confirm visible signs of bacterial or fungal growth.

RESULTS

MIC of MTA against the 2 microorganisms tested varied among the 4 preparations tested. WMTA-1 and WMTA-2 inhibited C. albicans growth at concentrations of 3.125 mg/10 mL and 25 mg/10 mL, respectively, and statistically significant differences were found between WMTA-1 and WMTA-2 (P < .001). WMTA-1 and WMTA-2 inhibited E. faecalis growth at concentrations of 12.5 mg/10 mL and 50 mg/10 mL, respectively, and statistically significant differences were found between WMTA-1 and WMTA-2 (P < .001). GMTA-1 and GMTA-2 inhibited E. faecalis growth at concentrations of 12.5 mg/10 mL and 3.125 mg/10 mL, respectively, and statistically significant differences were found between GMTA-1 and GMTA-2 (P < .001). Both GMTA-1 and GMTA-2 inhibited C. albicans growth at a concentration of 3.125 mg/10 mL and no statistical differences were found between the preparations. Subculture of the broth tubes in agar or brain heart infusion plates confirmed the turbidity test result.

CONCLUSION

The origin of MTA as well as the type of preparation may affect its antimicrobial characteristics. Clinicians should be aware of variations that may exist among such MTA preparations.

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.

Prevalence and clonal analysis of Porphyromonas gingivalis in primary endodontic infections

This study investigated the prevalence of Porphyromonas gingivalis in 62 teeth with primary endodontic infections by using a species-specific 16S rRNA gene-based nested polymerase chain reaction assay. P. gingivalis isolates recovered from 2 infected root canals were also analyzed for clonal diversity by using arbitrarily primed PCR. Overall, P. gingivalis was found in 48% of the samples. This species was specifically detected in 36% of canals of teeth with chronic apical periodontitis, in 46% of the cases of acute apical periodontitis, and in 67% of acute apical abscesses. P. gingivalis was significantly more frequent in abscess aspirates than in canals of teeth with chronic apical periodontitis (P < .05). Typing of colonies retrieved from 2 infected canals revealed 2 clones per individual. These findings confirmed that P. gingivalis can be an important endodontic pathogen, mostly associated with acute abscesses, and demonstrated that different clonal types of this species can colonize the root canal in the same individual.

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.

PCR-based identification of selected pathogens associated with endodontic infections in deciduous and permanent teeth

OBJECTIVE

The aim of the present study was to evaluate the presence of the selected pathogens in samples from deciduous and permanent tooth root canals by using PCR method and to determine the association of these organisms with clinical symptoms.

STUDY DESIGN

A total of 145 children, 5 to 13 years old, were involved in this study. The presence of selected pathogens (Actinomyces israelii, Candida albicans, Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus intermedius, Treponema denticola, Parvimonas micra, Tannerella forsythensis, Enterococcus faecium, Prevotella melaninogenica) in infected root canals was studied using PCR.

RESULTS

T. denticola (P = .012, .02) and E. faecalis (P = .012, .04) were highly associated with periapical radiolucency and previous pain, while P. gingivalis was associated with tenderness to percussion in both deciduous and permanent teeth (P = .01, .015).

CONCLUSION

The results of the present study confirm that certain species of microorganisms are associated with clinical signs and symptoms of endodontic disease in both deciduous and permanent teeth.

Microbiological evaluation of primary endodontic infections in teeth with and without sinus tract

AIM

To examine the microbiological status of primary endodontic infections in teeth with and without a sinus tract.

METHODOLOGY

Samples were collected by means of a size 15 H-type file and two sterile paper points from 30 cases of primary endodontic infections with (n = 15) or without (n = 15) a sinus tract. The presence of 40 bacterial species was determined by the checkerboard DNA-DNA hybridization method.

RESULTS

The species found at the highest levels and prevalence were Fusobacterium nucleatum sp. vincentii, Porphyromonas gingivalis, Veillonella parvula, Enterococcus faecalis, Campylobacter gracilis and Neisseria mucosa. Total bacterial counts were similar between teeth with (44 x 10(5)) and without (50 x 10(5)) a sinus tract (t-test: P > 0.05). E. faecalis, Streptococcus anginosus, Capnocytophaga sputigena and Capnocytophaga gingivalis had significantly higher counts in the absence of sinus tract (Mann-Whitney test, P < 0.05). Higher levels of P. gingivalis and Fusobacterium nucleatum sp. nucleatum were observed in cases with a sinus tract. Leptotrichia buccalis (OR = 1.83; CI 95%) and Porphyromonas endodontalis (OR = 2.15; CI 95%) were associated with an increased chance of subjects having a sinus tract.

CONCLUSIONS

Primary endodontic infections were associated with a large variety of bacterial species. Specific differences between the composition of the microbiota of primary root canal infections were observed in cases with or without a sinus tract.