Isolation and identification of Prevotella tannerae from endodontic infections

Oral microbiome of electronic cigarette users: A cross-sectional exploration

OBJECTIVE

Electronic cigarettes have increased in popularity globally. Vaping may be associated with oral symptoms and pathologies including dental and periodontal damage, both of which have an underlying microbial etiology. The primary aim of this pilot study, therefore, was to compare the oral microbiome of vapers and non-vapers.

SUBJECTS AND METHODS

This secondary data analysis had a cross-sectional comparative descriptive design and included data for 36 adults. Bacterial 16S rRNA genes were extracted and amplified from soft tissue oral swab specimens and taxonomically classified using the Human Oral Microbiome Database.

RESULTS

Data for 18 vapers and 18 non-vapers were included in this study. Almost 56% of the vapers also smoked conventional cigarettes. Beta diversity differences were identified between vapers and non-vapers. Vapers had a significantly higher relative abundance of an unclassified species of Veillonella compared with non-vapers. Dual users had higher alpha diversity compared with exclusive vapers. Beta diversity was also associated with dual use. Multiple OTUs were identified to be associated with dual use of e-cigarettes and conventional cigarettes.

CONCLUSIONS

Vapers exhibit an altered oral microbiome. Dual use of electronic cigarettes and conventional cigarettes is associated with the presence of several known pathogenic microbes.

Bacillus coagulans R11 maintained intestinal villus health and decreased intestinal injury in lead-exposed mice by regulating the intestinal microbiota and influenced the function of faecal microRNAs

Lead contamination is an environmental problem, especially in developing countries; due to the nondegradable characteristics of lead, it is easily deposited in human and animal bodies by the food chain. Probiotics are regarded as a good tool to remove lead ions in the intestine and maintain gut health conditions, but previous studies failed to elucidate the relationship among probiotics, the host and the gut microbiota. In the present study, B. coagulans R11 was employed as the "lead removal tool" in lead-exposed mouse, and the effects of B. coagulans R11 on intestinal cells, the microbiota and faecal microRNAs were tested. The results indicated that B. coagulans R11 had no negative effects on mouse intestine model cells and helped keep cells in a normal proliferation ratio and reduce the reactive oxygen species and apoptosis ratios under lead exposure conditions. An in vivo mouse experiment also showed that B. coagulans R11 feeding could reduce the intestinal villi damage caused by lead through adjusting the microbiota structure and function, such as increasing the genus abundance of Akkermansia and Alistipes, decreasing the genus abundance of Alloprevotella, Lachnospiraceae, Parabacteroides and Ruminiclostridium, and keeping the protein dltD existing. Host faecal microRNAs may be influenced by lead and B. coagulans R11, which may change the microbiota structure. Thus, B. coagulans R11 has the potential to be developed and considered as the probiotic that protects the host gut against villi damage and gut microbiota structure and function disorders during lead exposure.

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing

OBJECTIVE

The purpose of this study was to identify the endodontic microbiome in primary teeth with dental caries using high-throughput pyrosequencing and to establish data on the oral microbiome of primary teeth with endodontic infection.

METHODS

Ten primary teeth with dental caries and endodontic infection were included. Samples were collected from root canals using sterilized paper points and analyzed by pyrosequencing, based on the V1-V3 hypervariable region of the 16S rRNA gene. The data were analyzed using the CLcommunity software.

RESULTS

Analysis of the 10 samples yielded a total of 64,291 16S rRNA gene sequences. In total, 1586 OTUs (range, 91-235), six bacterial phyla, including unclassified, and 187 genera were assigned. At the genus level, Neisseria (group A), Acinetobacter (group B), and Fusobacterium (group C) were prominent. These predominant microorganisms were associated with the clinical condition and reflected the progression of endodontic infection in primary teeth.

CONCLUSIONS

This study revealed a relationship between the oral microbiome and endodontic infection in primary teeth. Additionally, anaerobic bacteria such as Fusobacterium species were dominant in the teeth with apical abscesses.

Controversies in Endodontics

Diseases of the dental pulp often have an infectious origin, and treatments are aimed to control infections of the root canal system. Endodontic treatment principles originally evolved on the basis of trial and error, and only in recent decades have scientific methods been adopted to support clinical strategies. Yet, relevant research on the disease processes, their diagnoses, and efficient treatment are rare in the endodontic literature. Hence, the advancement of biologically based knowledge significant to clinical endodontics has been slow. Therefore, many differences of opinion still prevail in this field of dentistry. This review highlights and analyzes the background of some of the more heavily debated issues in recent years. Specifically, it deals with disagreements regarding the clinical management of pulpal exposures by caries in the adult dentition, definitions of success and failure of endodontic therapy, and causes of and measures to control infections of the root canal system. Clearly, a most apparent gap in the published endodontic literature is the lack of randomized clinical trials that address the more significant controversial matters relating to the management of pulpal wounds, medication, and the number of appointments required for the treatment of infected root canals. However, trials in endodontics require extremely long follow-up periods if valid conclusions are to be generated. Therefore, it is not to be expected that there will be rapid solutions to these issues in the foreseeable future.

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease

Behçet's disease (BD) is characterized by recurrent oro-genital ulcers, mucocutaneous lesions, and serious organ involvement. We investigated the salivary microbiome in BD using high-throughput sequencing of the 16S rRNA V4 region. Stimulated saliva samples were collected from 31 BD patients and 15 healthy controls, and in 9 BD patients, a second saliva sample was collected following dental and periodontal treatment. Sequence analysis identified a total of 908 operational taxonomic units (OTUs) present across all samples. Patients had a microbial community structure that is significantly less diverse than healthy controls. The most overabundant species in BD was Haemophilus parainfluenzae, while the most depleted included Alloprevotella rava and species in the genus Leptotrichia. Periodontal treatment improved oral health indices in BD but had no short-term effect on bacterial community structure. Neither the BD-associated genetic risk locus within the HLA-B/MICA region nor being on immunosuppressive medications explained the differences between patients and controls.

Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species

The results of metagenomic studies have clearly established that bacteria of the genus Prevotella represent one of the important groups found in the oral cavity and large intestine of man, and they also dominate the rumen. They belong to the Bacteroidetes, a phylum well-known for its polysaccharide degrading potential that stems from the outer membrane-localized enzyme/binding protein complexes encoded in polysaccharide utilization loci (PULs). Dozens of Prevotella species have been described, primarily from the oral cavity, and many of them occur simultaneously at the same sites, but research on their ecological adaptation has been neglected. Therefore, in this study, the repertoires of PULs and carbohydrate acting enzymes (CAZYmes) found in Prevotella genomes were analyzed and it was concluded that the Prevotella species were widely heterogeneous in this respect and displayed several distinct adaptations with regard to the number, source and nature of the substrates apparently preferred for growth.

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.

Molecular detection of bacteria associated to dental caries in 4-12-year-old Tunisian children

The occurrence of several microbial species in the oral cavity of 4-12-year-old Tunisian children was investigated. Samples were taken from 158 children (81 caries actives and 77 caries free). Genomic DNA was extracted and analyzed for the presence of 17 microbial species using a polymerase chain reaction assay. All samples were positive for at least one of the target microbial strains. Streptococcus mutans was the most prevalent species (76.5%) detected in genomic DNA collected from carious lesions. Other prevalent species were Candida spp (63%), Streptococcus salivarius (59%) and Streptococcus oralis (42%). The frequency of Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus casei-group in caries lesions was 29.5%, 34.5% and 22% respectively. Pathogenic bacteria such as Staphylococcus aureus was found in 28.5% of carious lesion samples compared to 15.5% in the control. Frequency of Porphyromonas endodontali, Actinomyces radicidentis and Treponema denticola recovery did not differ significantly between origins of samples. PCR analysis of genomic DNA detect various oral bacteria that differ between caries actives and caries-free children. In addition, the association of same aciduric bacteria (S. mutans, S. salivarius, L. acidophilus) and caries formation was noticed.

[Anaerobic bacteria 150 years after their discovery by Pasteur]

In 2011 we celebrated the 150th anniversary of the discovery of anaerobic bacteria by Louis Pasteur. The interest of the biomedical community on such bacteria is still maintained, and is particularly focused on Clostridium difficile. In the past few years important advances in taxonomy have been made due to the genetic, technological and computing developments. Thus, a significant number of new species related to human infections have been characterised, and some already known have been reclassified. At pathogenic level some specimens of anaerobic microflora, that had not been isolated from human infections, have been now isolated in some clinical conditions. There was emergence (or re-emergence) of some species and clinical conditions. Certain anaerobic bacteria have been associated with established infectious syndromes. The virulence of certain strains has increased, and some hypotheses on their participation in certain diseases have been given. In terms of diagnosis, the routine use of MALDI-TOF has led to a shortening of time and a cost reduction in the identification, with an improvement directly related to the improvement of data bases. The application of real-time PCR has been another major progress, and the sequencing of 16srRNA gene and others is currently a reality for several laboratories. Anaerobes have increased their resistance to antimicrobial agents, and the emergence of resistance to carbapenems and metronidazole, and multi-resistance is a current reality. In this situation, linezolid could be an effective alternative for Bacteroides. Fidaxomicin is the only anti-anaerobic agent introduced in the recent years, specifically for the diarrhoea caused by C.difficile. Moreover, some mathematical models have also been proposed in relation with this species.

Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression

Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.

Impact of soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities

The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of (13) C-glucose and (13) C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (-0.001, -0.01 and -0.316 MPa) in 6 × 6 × 6 mm(3) cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.

Microbiologic profile of endodontic infections from HIV- and HIV+ patients using multiple-displacement amplification and checkerboard DNA-DNA hybridization

OBJECTIVE

To compare the microbiota of endodontic infections in necrotic pulp from HIV-negative and HIV-positive subjects.

MATERIALS AND METHODS

Root canal samples from necrotic pulp were collected from 40 HIV- and 20 HIV+ subjects. Pulps were amplified using multiple displacement amplification (MDA). Then, checkerboard DNA-DNA hybridization was employed to assess the levels of 107 microbial taxa. The percentage of DNA probe count and the percentage of teeth colonized by each test species were investigated. Significant differences between groups regarding proportions of taxa and prevalence of the test species were sought using the Mann-Whitney test and the Chi-square analysis, respectively.

RESULTS

The most prevalent taxa detected were Dialister pneumosintes, Stenotrophomonas maltophilia, Streptococcus sobrinus, Corynebacterium diphteriae, and Helicobacter pylori among HIV- subjects and D. pneumosintes, Prevotella tannerae, Porphyromonas gingivalis, Parvimonas micra, Prevotella nigrescens, and Corynebacterium diphtheriae among HIV+ individuals. D. pneumosintes, C. diphtheria, and C. albicans were the most abundant species in the HIV- group, whereas the predominant taxa in HIV+ samples were P. tannerae, D. pneumosintes and Olsenella uli. P. tannerae, O. uli, Veilonella dispar, Bacteroides fragilis, and Actinomyces meyeri were significantly more abundant in HIV+ samples.

CONCLUSIONS

There were significant differences in the prevalence and proportions of specific microbial taxa between HIV- and HIV+ individuals. The root canal microbiota may represent a reservoir of important oral and medical pathogens, mainly in HIV+ individuals.

Clustering behavior in microbial communities from acute endodontic infections

INTRODUCTION

Acute endodontic infections harbor heterogeneous microbial communities in both the root canal (RC) system and apical tissues. Data comparing the microbial structure and diversity in endodontic infections in related ecosystems, such as RC with necrotic pulp and acute apical abscess (AAA), are scarce in the literature. The aim of this study was to examine the presence of selected endodontic pathogens in paired samples from necrotic RC and AAA using polymerase chain reaction (PCR) followed by the construction of cluster profiles.

METHODS

Paired samples of RC and AAA exudates were collected from 20 subjects and analyzed by PCR for the presence of selected strict and facultative anaerobic strains. The frequency of species was compared between the RC and the AAA samples. A stringent neighboring clustering algorithm was applied to investigate the existence of similar high-order groups of samples. A dendrogram was constructed to show the arrangement of the sample groups produced by the hierarchical clustering.

RESULTS

All samples harbored bacterial DNA. Porphyromonas endodontalis, Prevotella nigrescens, Filifactor alocis, and Tannerela forsythia were frequently detected in both RC and AAA samples. The selected anaerobic species were distributed in diverse small bacteria consortia. The samples of RC and AAA that presented at least one of the targeted microorganisms were grouped in small clusters.

CONCLUSIONS

Anaerobic species were frequently detected in acute endodontic infections and heterogeneous microbial communities with low clustering behavior were observed in paired samples of RC and AAA.

Profiling of subgingival plaque biofilm microflora from periodontally healthy subjects and from subjects with periodontitis using quantitative real-time PCR

BACKGROUND AND OBJECTIVE

Qualitative and quantitative changes of the subgingival plaque biofilm microflora in periodontal pockets are thought to be associated with the development and progression of periodontitis. The aims of the present study were to quantify the proportions of nine periodontitis-associated bacterial species and four Streptococcus species in subgingival plaque, and to evaluate their relationship with periodontitis quantitatively.

MATERIAL AND METHODS

Subgingival plaque samples were obtained from 12 periodontally healthy subjects and from 28 patients with periodontitis. The amounts of total and target bacteria were measured by quantitative real-time PCR using universal and species-specific primers, respectively.

RESULTS

The proportion of total obligate anaerobes was found to be higher in subjects with periodontitis than in periodontally healthy subjects (p < 0.05). Among obligate anaerobes, Tannerella forsythia (2.04 +/- 5.27%, p < 0.05), Porphyromonas gingivalis (0.54 +/- 1.41%) and Eubacterium saphenum (0.30 +/- 0.96%) were detected at high proportions in subjects with periodontitis, but not in periodontally healthy subjects. By contrast, the proportion of total streptococci was lower in subjects with periodontitis (p < 0.05). Specifically, the proportion of T. forsythia, P. gingivalis or E. saphenum increased (>or= 2.78%) and the proportion of Streptococcus species decreased to virtually undetectable levels, in subjects with periodontitis.

CONCLUSION

Obligate anaerobes, including T. forthysia, P. gingivalis and E. saphenum, were identified predominantly in microflora from subjects with periodontitis, whereas Streptococcus species were identified predominantly in microflora from periodontally healthy subjects, suggesting a change in the subgingival environment that resulted in conditions more suitable for the survival of obligate anaerobes. The proportion of these obligate anaerobes in the subgingival plaque of subjects with periodontitis appears to be associated with the status of human periodontitis.

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.

Development of a novel PCR assay for detection of Prevotella oris in clinical specimens

Prevotella oris is a nonpigmented, Gram-negative, anaerobic bacterium that has been associated with several serious oral and systemic infections. Prevotella oris has been identified in clinical specimens by bacterial culture and biochemical tests, which are generally unreliable. The aim of this study was to develop a PCR assay for the direct detection of P. oris in clinical specimens. PCR primers specific for P. oris were identified by alignment of bacterial 16S rRNA genes from closely related species and selection of PCR primers specific for P. oris at their 3' ends. Amplification of a 1110-bp product indicated PCR positivity for P. oris. The primers were shown to be specific for P. oris DNA, because no PCR products were obtained when DNA from other oral bacteria, including closely related Prevotella species, were used as test species, and this was confirmed by digestion of PCR products with RsaI and MnlI. Prevotella oris DNA was detected in 17 (36.2%) of 47 pus samples from subjects with dentoalveolar abscesses and in all three pus samples from subjects with spreading odontogenic infections. This PCR assay provides a sensitive, specific and reliable method for identifying P. oris in clinical specimens.

Use of multiple-displacement amplification and checkerboard DNA-DNA hybridization to examine the microbiota of endodontic infections

Multiple-displacement amplification (MDA) has been used to uniformly amplify bacterial genomes present in small samples, providing abundant targets for molecular analysis. The purpose of this investigation was to combine MDA and checkerboard DNA-DNA hybridization to examine the microbiota of endodontic infections. Sixty-six samples were collected from teeth with endodontic infections. Nonamplified and amplified samples were analyzed by checkerboard DNA-DNA hybridization for levels and proportions of 77 bacterial taxa. Counts, percentages of DNA probe counts, and percentages of teeth colonized for each species in amplified and nonamplified samples were computed. Significance of differences for each species between amplified and nonamplified samples was sought with Wilcoxon signed-rank test and adjusted for multiple comparisons. The amount of DNA in the samples ranged from 6.80 (+/- 5.2) ng before to 6.26 (+/- 1.73) mug after MDA. Seventy of the 77 DNA probes hybridized with one or more of the nonamplified samples. All probes hybridized with at least one sample after amplification. Most commonly detected species at levels of >10(4) in both amplified and nonamplified samples were Prevotella tannerae and Acinetobacter baumannii at frequencies between 89 and 100% of samples. The mean number of species at counts of >10(4) in amplified samples was 51.2 +/- 2.2 and in nonamplified samples was 14.5 +/- 1.7. The endodontic microbiota was far more complex than previously shown, although microbial profiles at teeth with or without periradicular lesions did not differ significantly. Species commonly detected in endodontic samples included P. tannerae, Prevotella oris, and A. baumannii.

A new checkerboard panel for testing bacterial markers in periodontal disease

BACKGROUND/AIMS

Various microbiological methods have been used for testing bacterial markers for periodontitis and periodontal disease progression. Most studies have used only a limited number of well recognized bacterial species. The purpose of the present study was to evaluate the association of 13 more recently identified bacterial species in a new panel in comparison with 12 previously more recognized periodontotopathogens ('old panel') using the 'checkerboard' DNA-DNA hybridization method.

METHODS

Fifty individuals were chosen who showed at least one site with a probing pocket depth of 6 mm or more (disease) and bleeding on probing and at least one site with a probing pocket depth of 3 mm and without bleeding on probing (health). One diseased and one healthy site on each individual were sampled with the paperpoint technique and the samples were processed in the checkerboard technique against deoxigenin-labeled whole genomic probes to 25 subgingival species representing 12 well recognized and 13 newly identified periodontitis associated species.

RESULTS

Twenty-four (out of 25) species were detected more frequently in the subgingival plaque of diseased than healthy sites both at score 1 (> 10(4)) and score 3 (> 10(5)). A significant difference at the higher score (score 3) was noticed for all species of the old panel except for three (Streptococcus intermedius, Selenomonas noxia, and Eikenella corrodens). Of the species in the new panel only Prevotella tannerae, Filifactor alocis, and Porphyromonas endodontalis showed a statistical significant difference between diseased and healthy sites.

CONCLUSION

It was concluded that P. tannerae, F. alocis, and P. endodontalis should be added to the 12 species used for routine diagnostics of periodontitis-associated bacterial flora.

Detection of novel oral species and phylotypes in symptomatic endodontic infections including abscesses

This study was undertaken to investigate the occurrence of several uncultivated phylotypes and newly named bacterial species in symptomatic endodontic infections. Samples taken from cases clinically diagnosed as acute periradicular abscesses or acute periradicular periodontitis were surveyed for the presence of 12 taxa by means of a 16S rRNA-gene-based nested or hemi-nested PCR assay. The most prevalent of the target taxa were Dialister invisus, Olsenella uli, Granulicatella adiacens, and Synergistes clones BA121 and E3_33. Findings revealed that novel phylotypes and newly named species can take part in the microbiota associated with symptomatic endodontic infections and a pathogenetic role is suspected.

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.

Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia and Prevotella nigrescens in endodontic lesions detected by culture and by PCR

he aim of this study was to investigate the presence of four black-pigmented bacteria, Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia and Prevotella nigrescens, in endodontic infections by culture and polymerase chain reaction (PCR) analyses. Microbial samples were obtained from 50 teeth with untreated necrotic pulps (primary infection) and from 50 teeth with failing endodontic treatment (secondary infection). Microbiological strict anaerobic techniques were used for serial dilution, plating, incubation, and identification. For PCR detection, the samples were analyzed using species-specific primers of 16S rDNA and the downstream intergenic spacer region. Culture and PCR detected the test species in 13/100 and 50/100 of the study teeth, respectively. The organisms were cultured from 11/50 (22%) of primarily infected root canal samples and from 2/50 (4%) of secondary root canal samples. PCR detection identified the target species in 32/50 (64%) and 18/50 (36%) of primary and secondary infections, respectively. P. gingivalis was rarely isolated by culture methods (1%), but was the most frequently identified test species by PCR (38%). Similarly, P. endodontalis was not recovered by culture from any tooth studied, but was detected by PCR in 25% of the sampled teeth. PCR-based identification also showed higher detection rates of P. intermedia (33%) and P. nigrescens (22%) than culture (13%). In conclusion, P. gingivalis, P. endodontalis, P. intermedia, and P. nigrescens were identified more frequently in teeth with necrotic pulp than in teeth with failing endodontic treatment. Also, a higher frequency of black-pigmented species was detected by PCR than by culture.

PCR-based diagnostics for anaerobic infections

Conventional methods to identify anaerobic bacteria have often relied on unique clinical findings, isolation of organisms, and laboratory identification by morphology and biochemical tests (phenotypic tests). Although these methods are still fundamental, there is an increasing move toward molecular diagnostics of anaerobes. In this review, some of the molecular approaches to anaerobic diagnostics based on the polymerase chain reaction (PCR) are discussed. This includes several technological advances in PCR-based methods for the detection, identification, and quantitation of anaerobes including real-time PCR which has been successfully used to provide rapid, quantitative data on anaerobic species on clinical samples. Since its introduction in the mid-1980s, PCR has provided many molecular diagnostic tools, some of which are discussed within this review. With the advances in micro-array technology and real-time PCR methods, the future is bright for the development of accurate, quantitative diagnostic tools that can provide information not only on individual anaerobic species but also on whole communities.

Detection frequency of periodontitis-associated bacteria by polymerase chain reaction in subgingival and supragingival plaque of periodontitis and healthy subjects

The aim of this study was to compare the detection frequencies of 25 bacterial species in subgingival and supragingival plaque of 18 untreated periodontitis subjects and 12 periodontally healthy subjects. Genomic DNA was extracted from subgingival and supragingival plaque samples, and bacterial detection was performed by polymerase chain reaction of the 16S rRNA genes. Fourteen bacteria showed no relationship with periodontitis, and 11 of these 14 species were frequently detected (> or =50%) in subgingival plaque in both periodontitis and healthy subjects. Nine bacteria such as Eubacterium saphenum, Prevotella intermedia, and Treponema denticola seemed to be related to periodontitis; their detection frequencies in subgingival plaque samples were higher in periodontitis than in healthy subjects, but these differences were not statistically significant by multiple comparisons (0.002< or =P<0.05). Two species (Mogibacterium timidum and Porphyromonas gingivalis) were detected significantly more frequently in subgingival plaque of periodontitis subjects than of healthy subjects (P<0.002), with P. gingivalis being detected only in periodontitis subjects, suggesting that these two species are closely related to periodontitis. There were no significant differences in the detection frequencies of the 25 bacteria between subgingival and supragingival plaque, suggesting that the bacterial flora of supragingival plaque reflects that of subgingival plaque.

The clinical significance of anaerobic bacteria in acute orofacial odontogenic infections

A review of the literature on orofacial odontogenic infections indicates that the underlying microflora is typically polymicrobial, predominantly involving strictly anaerobic gram-positive cocci and gram-negative rods, along with facultative and microaerophilic streptococci. Although no single species has been consistently implicated in all of these infections, the pathogenic potential of some of these organisms has been documented by many studies. This potential can be explained by a number of virulence factors demonstrated in anaerobic bacteria, as well as by synergistic interrelationships with other members of the infectious flora. Awareness of the anaerobic component of orofacial odontogenic infections dictates to a large extent the selection of antimicrobial therapy, mainly because of the frequency of beta-lactamase production by anaerobic gram-negative rods.

Selected Endodontic Pathogens in the Apical Third of Infected Root Canals: A Molecular Investigation

Bacteria located at the apical portion of the root canals are conceivably in a strategic position to induce damage to the periradicular tissues and resulting inflammatory diseases. This study sought to investigate the prevalence of 11 selected putative endodontic pathogens in the apical third of infected root canals associated with periradicular lesions. The apical root portion of 23 extracted teeth with carious pulpal exposures and attached periradicular lesions was sectioned, and the root canals were sampled for microbiological investigation. DNA was extracted from the samples and analyzed for the presence of 11 bacterial species using a nested polymerase chain reaction assay. The results showed that Pseuramibacter alactolyticus occurred in 10 cases (44%), Treponema denticola in 6 (26%), Fusobacterium nucleatum in 6 (26%), Porphyromonas endodontalis in 4 (17%), Filifactor alocis in 2 (9%), Dialister pneumosintes in 1 (4%), Porphyromonas gingivalis in 1 (4%), and Tannerella forsythensis in 1 (4%). No sample yielded Prevotella intermedia, Prevotella nigrescens, or Campylobacter rectus. Of the samples examined, 17 were positive for at least 1 of the target species. Occurrence of these bacterial species in the apical third of infected root canals suggests that they can be involved in causation of periradicular lesions.

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.

Occurrence of Actinomyces in infections of endodontic origin

Species of Actinomyces have been associated with endodontic treatment that failed to heal. In this study polymerase chain reaction was used with a pair of universal primers for Actinomyces and species-specific primers to evaluate the contents of infected root canals and aspirates from abscesses or cellulitis for the presence of Actinomyces israelii, A. naeslundii, and A. viscosus. DNA was extracted from 131 clinical samples. DNA from 2 of the original 131 samples was not available for polymerase chain reaction with the universal primer for Actinomyces and A. naeslundii. DNA reacting with the universal primer for Actinomyces was detected in 72 of 129 (55.8%) clinical samples. Of those 41 of 51 (80.4%) were from infected root canals, 22 of 48 (45.8%) were from abscesses, and 9 of 30 (30%) were associated with cellulitis. A. viscosus was detected in 42 of 131 (32.1%) clinical samples. Of those 31 of 52 (59.6%) were from infected root canals, 6 of 43 (14%) were from abscesses, and 5 of 36 (13.9%) were associated with cellulitis. A. israelii was detected in 31 of 131 (23.7%) clinical samples. Of those 14 of 52 (26.9%) were from infected root canals, 11 of 43 (25.6%) were from abscesses, and 6 of 36 (16.7%) were associated with cellulitis. A. naeslundii was detected in 11 of 131 (8.5%) clinical samples. Of those 7 of 51 (13.7%) were from infected root canals, 2 of 48 (4.2%) were from abscesses, and 2 of 30 (6.7%) were associated with cellulitis.

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.

Peptostreptococcus micros in primary endodontic infections as detected by 16S rDNA-based polymerase chain reaction

A 16S rDNA-based polymerase chain reaction (PCR) method was used to detect Peptostreptococcus micros in primary root canal infections. Samples were collected from 50 teeth having carious lesions, necrotic pulps, and different forms of periradicular diseases. DNA extracted from the samples was amplified using the PCR assay, which yielded a specific fragment of P. micros 16S rDNA. P. micros was detected in 6 of 22 root canals associated with asymptomatic chronic periradicular lesions (27.3%), 2 of 8 teeth with acute apical periodontitis (25%), and 6 of 20 cases of acute periradicular abscess (30%). In general, P. micros was found in 14 of 50 cases (28%). There was no correlation between the presence of P. micros and the occurrence of symptoms. Findings suggested that P. micros can be involved in the pathogenesis of different forms of periradicular lesions.

Identification of bacteria in acute endodontic infections and their antimicrobial susceptibility

OBJECTIVE

The purpose of the study was to identify the bacterial composition of the microbiota from acute endodontic abscesses/cellulitis and their antimicrobial susceptibilities.

STUDY DESIGN

Purulence from 17 patients with acute endodontic abscesses/cellulitis was obtained by needle aspiration and processed under anaerobic conditions. Bacteria were isolated and identified by biochemical or molecular methods. The antimicrobial susceptibility of isolated bacteria was determined by using the Etest.

RESULTS

All 17 aspirates contained a mix of microorganisms. A total of 127 strains of bacteria were isolated. Of 127 strains, 80 strains were anaerobes and 47 strains were aerobes. The mean number of strains per sample was 7.5 (range, 3 to 13). The average number of viable bacteria was 6.37 x 10(7) (range, 10(4) to 10(8)) colony-forming units/mL. Strict anaerobes and microaerophiles were the dominant bacteria in 82% (14 of 17) of the cases. The genera of bacteria most frequently encountered were Prevotella and Streptococcus. Prevotella and Peptostreptococcus were frequently found to dominate the mixture. The combination of Prevotella and Streptococcus was found in 53% (9 of 17). The previously reported uncultured Prevotella clone PUS9.180 was frequently identified. The percentage of bacteria susceptible/intermediate for each antibiotic in this study was penicillin V, 81% (95 of 118); metronidazole, 88% (51 of 58); amoxicillin, 85% (100 of 118); amoxicillin + clavulanic acid, 100% (118 of 118); and clindamycin, 89% (105 of 118).

CONCLUSIONS

The present results confirm the existence of mixed infection with the predominance of anaerobic bacteria in acute endodontic abscesses/cellulitis. The frequency of uncultured Prevotella clone PUS9.180 suggests the possible key role of this Prevotella species in acute endodontic infections. Penicillin V still possesses antimicrobial activity against the majority of bacteria isolated from acute endodontic infections. However, if penicillin V therapy has failed to be effective, the combination of penicillin V with metronidazole or amoxicillin with clavulanic acid is recommended. Switching to clindamycin is another good alternative.

Comparison of 16S rDNA-based PCR and checkerboard DNA-DNA hybridisation for detection of selected endodontic pathogens

Molecular methods have been used recently to investigate the bacteria encountered in human endodontic infections. The aim of the present study was to compare the ability of a 16S rDNA-based PCR assay and checkerboard DNA-DNA hybridisation in detecting Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Peptostreptococcus micros, Porphyromonas endodontalis, Por. gingivalis and Treponema denticola directly from clinical samples. Specimens were obtained from 50 cases of endodontic infections and the presence of the target species was investigated by whole genomic DNA probes and checkerboard DNA-DNA hybridisation or taxon-specific oligonucleotides with PCR assay. Prevalence of the target species was based on data obtained by each method. The sensitivity and specificity of each molecular method was compared with the data generated by the other method as the reference--a value of 1.0 representing total agreement with the chosen standard. The methods were also compared with regard to the prevalence values for each target species. Regardless of the detection method used, T. denticola, Por. gingivalis, Por. endodontalis and B. forsythus were the most prevalent species. If the checkerboard data for these four species were used as the reference, PCR detection sensitivities ranged from 0.53 to 1.0, and specificities from 0.5 to 0.88, depending on the target bacterial species. When PCR data for the same species were used as the reference, the detection sensitivities for the checkerboard method ranged from 0.17 to 0.73, and specificities from 0.75 to 1.0. Accuracy values ranged from 0.6 to 0.74. On the whole, matching results between the two molecular methods ranged from 60% to 97.5%, depending on the target species. The major discrepancies between the methods comprised a number of PCR-positive but checkerboard-negative results. Significantly higher prevalence figures for Por. endodontalis and T. denticola were observed after PCR assessment. There was no further significant difference between the methods with regard to detection of the other target species.

Dialister pneumosintes can be a suspected endodontic pathogen

OBJECTIVE

Dialister pneumosintes is a nonmotile, nonfermentative, non-spore-forming, obligately anaerobic, gram-negative bacillus that has been associated with some infections in the human body. A species-specific nested polymerase chain reaction assay was used to investigate the occurrence of D pneumosintes in primary root canal infections.

STUDY DESIGN

Samples were collected from 32 teeth with carious lesions, necrotic pulps, and radiographic evidence of periradicular bone destruction. Twenty-two teeth were asymptomatic, and 10 cases were diagnosed as acute apical periodontitis. DNA extracted from the samples was initially amplified with universal 16S ribosomal DNA primers. A second round of amplification used the first polymerase chain reaction products to specifically detect D pneumosintes.

RESULTS

This bacterial species was detected in 17 of 22 asymptomatic cases (77.3%) and in 4 of 10 root canals associated with acute apical periodontitis (40%). No relationship was found between the presence of this bacterial species and the occurrence of symptoms. In general, D pneumosintes was detected in 21 of 32 root canal samples (65.6%).

CONCLUSION

This study is the first to report a high prevalence of D pneumosintes in root canal infections of humans. Because of this high prevalence and the apparent pathogenicity of the microorganism, we suggest the inclusion of D pneumosintes in the selected group of putative endodontic pathogens.

Endodontic infections: concepts, paradigms, and perspectives

Overwhelming evidence indicates that periradicular diseases are infectious disorders. The question now is no longer whether microorganisms are involved in the pathogenesis of such diseases, but which specific microbial species are. The list of microorganisms involved in periradicular diseases keeps expanding and has the potential to become increasingly more accurate during the next few years. Molecular methods have contributed significantly to the knowledge about the microbial species involved. Undoubtedly, a great deal of additional research is needed to define the specific role played by suspected endodontic pathogens in the etiology of each form of periradicular disease and to determine the best therapeutic measures for the pathogen's eradication. In addition, there is an emergent need to define markers that permit the clinician to know when he or she should conclude the treatment and to predict the outcome of the treatment. Although endodontic procedures and some acute endodontic infections can cause bacteremia, there is no clear evidence that microorganisms from the root canal can cause diseases in remote sites of the body. However, there is a risk in some compromised individuals, and prophylactic measures should be taken. Prescription of systemic antibiotics in endodontic therapy is rarely necessary. Because of the emergence of bacterial resistance against most known antibiotics, their use in endodontics should be highly limited and restricted to a few cases.

Quantitative microbiological study of human carious dentine by culture and real-time PCR: association of anaerobes with histopathological changes in chronic pulpitis

The bacteria found in carious dentine were correlated with the tissue response of the dental pulps of 65 teeth extracted from patients with advanced caries and pulpitis. Standardized homogenates of carious dentine were plated onto selective and nonselective media under anaerobic and microaerophilic conditions. In addition, real-time PCR was used to quantify the recovery of anaerobic bacteria. Primers and fluorogenic probes were designed to detect the total anaerobic microbial load, the genera Prevotella and Fusobacterium, and the species Prevotella melaninogenica, Porphyromonas endodontalis, Porphyromonas gingivalis, and Micromonas (formerly Peptostreptococcus) micros. The pulpal pathology was categorized according to the cellular response and degenerative changes. Analysis of cultured bacteria showed a predominance of gram-positive microorganisms, particularly lactobacilli. Gram-negative bacteria were also present in significant numbers with Prevotella spp., the most numerous anaerobic group cultured. Real-time PCR analysis indicated a greater microbial load than that determined by colony counting. The total number of anaerobes detected was 41-fold greater by real-time PCR than by colony counting, while the numbers of Prevotella and Fusobacterium spp. detected were 82- and 2.4-fold greater by real-time PCR than by colony counting, respectively. Real-time PCR also identified M. micros, P. endodontalis, and P. gingivalis in 71, 60, and 52% of carious samples, respectively. Correlation matrices of the real-time PCR data revealed significant positive associations between M. micros and P. endodontalis detection and inflammatory degeneration of pulpal tissues. These anaerobes have been strongly implicated in endodontic infections that occur as sequelae to carious pulpitis. Accordingly, the data suggest that the presence of high levels of these bacteria in carious lesions may be indicative of irreversible pulpal pathology.

Direct amplification of rRNA gene sequences for identification of selected oral pathogens in root canal infections

AIM

The purpose of this study was to assess the prevalence of selected oral pathogens in root canal infections and their relationship with symptoms using a highly sensitive technique, the polymerase chain reaction.

METHODOLOGY

Samples were obtained from 91 infected teeth associated with periradicular lesions, including cases of acute periradicular abscesses. DNA was extracted from the samples and analysed for the presence of target microbial species using a PCR-based identification assay.

RESULTS

All samples were positive for the presence of bacteria. Streptococcus anginosus group was detected in 16.7%, Fusobacterium nucleatum in 14.3%, and Bacteroides forsythus in 7.1% of the abscess samples. No pus sample yielded Actinomyces israelii, Actinobacillus actinomycetemcomitans or fungal species. In general, B. forsythus was found in 20% of the cases (16 of 80), S. anginosus in 12% (6 of 50), F. nucleatum in 10% (6 of 60) and A. israelii in 5% (two of 40). A. actinomycetemcomitans was not detected in any case. Fungi were present in only one of 50 cases (2%). There was no correlation between the species and symptoms.

CONCLUSIONS

Direct molecular approaches appear to be a valuable tool for the rapid and reliable diagnosis of infectious diseases, as well as for research purposes. There was no correlation between target microbial species and symptoms.