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

Identification of bacteria associated with spreading odontogenic infections by 16S rRNA gene sequencing

OBJECTIVE

To determine the bacterial species associated with spreading odontogenic infections (SOIs).

STUDY DESIGN

Pus samples from 4 cases of SOI were analyzed by microbiological culture methods for the presence of bacteria, and by polymerase chain reaction (PCR) amplification, cloning, and sequencing of bacterial 16S rRNA genes.

RESULTS

Culture methods identified species from the genera Prevotella, Streptococcus, and Fusobacterium, as well as anaerobic streptococci. Molecular detection methods identified a far more diverse microflora. The predominant genus detected was Prevotella, representing 102 (50.2%) of 203 clones analyzed. Prevotella oris was the most abundant species identified, representing 45 (22.2%) of 203 clones analyzed. Twelve clones (5.9%) represented uncultivable species, namely Prevotella PUS9.180, an uncultured Peptostreptococcus species, and an uncultured bacterium belonging to the Bacteroidetes phylum.

CONCLUSIONS

Prevotella species may play an important role in SOIs, and further work to examine in more detail the pathogenicity determinants of these organisms and associated host responses is warranted.

On the use of denaturing gradient gel electrophoresis approach for bacterial identification in endodontic infections

Bacteria in infected root canals of teeth evincing chronic apical periodontitis lesions were identified by a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach. DNA was extracted from root canal samples, and part of the 16S rRNA gene of all bacteria was amplified by PCR and separated by DGGE, generating banding patterns representative of the community structure. Twenty visible bands were cut out of the gel, re-amplified, and sequenced to provide identification. Sequencing analysis revealed the presence of both cultivable and as-yet-uncultivated species in the samples analyzed, including representatives of the genera Fusobacterium, Bacteroides, Dialister, Synergistes, Prevotella, Eubacterium and Peptostreptococcus. Unambiguous identification was not always possible and the method's limitations are discussed. In general, the findings showed that PCR-DGGE can be useful for the identification of both cultivable and as-yet-uncultivated bacteria in endodontic infections.

Culture-independent detection of Eikenella corrodens and Veillonella parvula in primary endodontic infections

Eikenella corrodens and Veillonella parvula are normal cultivable inhabitants of the oral cavity but their presence in endodontic infections has not been as common as it could be anticipated. This might have been because of shortcomings of culture techniques when it comes to bacterial isolation or identification. The present study intended to survey samples from primary endodontic infections for the presence of E. corrodens and V. parvula using a culture-independent 16S rRNA gene-based nested PCR protocol. Genomic DNA was isolated directly from samples taken from different forms of periradicular lesions, and the presence of E. corrodens and V. parvula was determined by nested PCR. Specificity for each primer pair was confirmed by sequence analysis of PCR products from positive clinical samples. V. parvula and E. corrodens were, respectively, detected in 33% and 14% of the root canals associated with chronic apical periodontitis. Both V. parvula and E. corrodens were found in 10% of the cases diagnosed as acute apical periodontitis. V. parvula and E. corrodens were detected in 21% and 26% of the samples from acute apical abscesses, respectively. In general, species-specific nPCR allowed the detection of V. parvula in 24% and E. corrodens in 18% of the samples taken from primary endodontic infections. Findings confirmed that V. parvula and E. corrodens can take part in the microbiota of primary endodontic infections, but in prevalence values somewhat higher when compared to most of the previous culture studies that had reported recovery of these species.

Catonella morbi and Granulicatella adiacens: new species in endodontic infections

OBJECTIVE

This study intended to examine samples from primary endodontic infections for the presence of Catonella morbi and Granulicatella adiacens, 2 species that have been recently suggested to be involved with infections in other oral sites.

STUDY DESIGN

Genomic DNA was isolated directly from samples taken from teeth with different forms of apical periodontitis, and a devised culture-independent 16S rRNA gene-based heminested PCR assay was used to determine the prevalence of these 2 target species. Species-specific primers were developed by aligning closely related 16S rRNA gene sequences. Species-specificity for each primer pair was confirmed by running PCR against a panel of oral bacteria and by sequencing of DNA from representative positive samples.

RESULTS

C morbi and G adiacens were detected in 33% and 19%, respectively, of the root canals associated with chronic apical periodontitis; 30% and 10%, respectively, of the cases diagnosed as acute apical periodontitis, and 16% and 11%, respectively, of the pus samples taken from acute apical abscesses. Overall, C morbi occurred in 26% and G adiacens in 14% of the samples taken from primary endodontic infections.

CONCLUSIONS

Our findings demonstrate that C morbi and G adiacens can take part in the microbiota associated with primary endodontic infections, and their specific role in the disease process warrants further elucidation.