Oligonucleotide probes to the 16S ribosomal RNA: implications of sequence homology and secondary structure with particular reference to the oral species Prevotella intermedia and Prevotella nigrescens

Multiplex polymerase chain reaction assay for simultaneous detection of black-pigmented Prevotella species in oral specimens

Prevotella species are a major component of the oral microflora and some have been implicated in various forms of periodontal disease. Despite the importance of understanding the prevalence of these organisms in the oral microflora, no rapid, simultaneous detection system for these species has been reported. This study developed a multiplex polymerase chain reaction assay for the simultaneous detection of four oral black-pigmented Prevotella species in various oral specimens. This assay will be useful for determining the prevalence of these organisms in the oral ecosystem. Furthermore, this assay system should prove a useful tool for analyzing the role of black-pigmented Prevotella species in the mouth.

Comparison of microbial cultivation and a commercial PCR based method for detection of periodontopathogenic species in subgingival plaque samples

OBJECTIVES

Microbiological laboratory procedures are involved in diagnosis and therapy control of progressive and refractory forms of periodontitis. In recent years techniques have been developed based on the detection of nucleic acids. The purpose of this study was to validate the commercially available micro-Dent(R) test which employs probes for A. actinomycetemcomitans, P. gingivalis, P. intermedia, B. forsythus and T. denticola.

METHODS

122 plaque samples obtained from periodontal pockets with various depths from 33 early onset periodontitis (EOP) patients and 15 periodontally healthy subjects were analysed by cultivation and the microDent(R) kit.

RESULTS

Both cultivation and the nucleic acid based assay showed a positive correlation of pocket depth with the frequency and quantity of periodontopathogenic species. T. denticola was found only in pockets > 4 mm in EOP patients. Comparison of the two methods revealed that the microDent(R) kit identified both P. gingivalis and B. forsythus more often than did the cultivation method.

CONCLUSIONS

Nucleic acid techniques should replace cultivation methods as gold standard in microbiological diagnosis of progressive periodontitis. The micro-Dent(R) kit can be recommended for microbiological laboratories analysing subgingival plaque samples.

Detection of Prevotella intermedia in subgingival plaque of adult periodontitis patients by polymerase chain reaction

A PCR assay was developed that could specifically amplify DNA from the periodontal pathogen Prevotella intermedia. A pair of primers was selected from regions of the 16S rRNA gene of P. intermedia that were both divergent in sequence at their 3' ends with respect to the corresponding regions of the 16S rRNA gene of P. nigrescens, its most closely related species, and used in the PCR assay. Positivity was indicated by amplification of an 855 bp product. Using purified genomic DNA from these 2 species, assay conditions were determined under which only P. intermedia DNA and not P. nigrescens DNA was amplifiable. Absolute specificity of the assay was confirmed by the fact that no amplification products were obtained when using DNA from several other important periodontal organisms. The optimized PCR assay was used to identify P. intermedia in subgingival plaque samples of patients with adult periodontitis. Confirmation of amplification of P. intermedia DNA was achieved by digestion of PCR products with the restriction endonuclease RsaI, which gives different restriction patterns for P. intermedia and P. nigrescens. Of the 97 samples analysed, 38 (39%) were positive for P. intermedia. The results obtained confirm P. intermedia as a possible aetiological agent of adult periodontitis. Additionally, PCR primers targeting the corresponding region of the 16S rRNA gene of P. nigrescens were shown to be specific for the organism when used in a PCR assay, although P. nigrescens was not detectable in any of the subgingival plaques analysed.

RAPD fingerprinting for the distinction ofPrevotella intermediasensu stricto fromPrevotella nigrescens

A collection of 70 oral strains including reference strains and clinical isolates identified as Prevotella intermedia sensu lato was constituted to cover a large clinical and geographical diversity. Electrophoresis of the enzyme malate dehydrogenase allowed the identification of the 70 study strains as Prevotella intermedia sensu stricto (n= 36), Prevotella nigrescens (n= 31) and three unclassified strains. By using four primers, DNA fingerprints were generated from 20 strains as random amplified polymorphic DNA (RAPD). Matching co-migrating amplicon positions by pairwise comparison allowed the clustering of the fingerprints as two groups coincident with the P. intermedia/P. nigrescens assignment by enzyme electrophoresis of malate dehydrogenase. Our data suggest that isolates identified asP. intermedia sensu lato by conventional criteria can be speciated asP. intermedia sensu stricto or P. nigrescens by RAPD fingerprinting.

PCR-DNA probe assays for identification and detection of Prevotella intermedia sensu stricto and Prevotella nigrescens

The purpose of this study was to construct PCR-DNA probe assays specific for Prevotella intermedia sensu stricto and Prevotella nigrescens based on the ability of randomly amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific markers. The strategy included four steps: (i) construction of first-generation DNA probes from a 850-bp RAPD marker for P. intermedia sensu stricto and a 1,300-bp RAPD marker for P. nigrescens, (ii) cloning and sequencing of each RAPD marker, (iii) designing of primer pairs flanking specific internal sequences of 754 bp for P. intermedia sensu stricto and of ca. 1,100 bp for P. nigrescens, and (iv) synthesis (by PCR amplification) and digoxigenin labeling of quantities of DNA probes 754 and ca. 1,100 bp in size. The PCR-DNA probe assays combine either PCR amplification of a 754-bp specific sequence in the genomic DNA of strains of P. intermedia sensu stricto and hybridization with the 754-bp digoxigenin-labeled probe or amplification of a ca. 1,100-bp sequence of P. nigrescens and hybridization with the ca. 1,100-bp probe. Specific hybridization was observed with the amplified DNAs from 25 strains of P. intermedia and 24 strains of P. nigrescens, and no reaction was observed with the PCR products from 20 foreign species. The PCR-DNA probe assays described here should allow a highly specific and sensitive detection of P. intermedia sensu stricto and P. nigrescens in mixed infections.

Optimized oligonucleotides for the differentiation of Prevotella intermedia and Prevotella nigrescens

The gram-negative, anaerobic bacterium Prevotella intermedia plays an important role in the progression of periodontitis, whereas the etiological role of the closely related but phenotypically indistinguishable species Prevotella nigrescens is controversial. To differentiate between these species properly, 16S rDNA/RNA directed, computer-optimized oligonucleotides were designed and tested with 26 P. intermedia, 26 P. nigrescens and a number of closely and more distantly related strains. The oligonucleotides were used as primers in a polymerase chain reaction and could be demonstrated to be species specific with a detection limit of 50 bacterial cells, which could also be detected when diluted 1:10(5) with different plaque bacteria. In addition, the described oligonucleotides were digoxigenin-labeled at the 3' end and used as DNA probes in a dot blot hybridization assay. This assay, although slightly less sensitive than the polymerase chain reaction-based method, gave species-specific reactions and also allowed (semi-)quantification of bacterial cells in clinical specimens.