HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by SIQUEIRA, J. F. Articles by SANTOS, K. R. N. Search for Related Content PubMed PubMed Citation Articles by SIQUEIRA, J. F. Articles by SANTOS, K. R. N. Agricola Articles by SIQUEIRA, J. F. Articles by SANTOS, K. R. N.

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

Institute of Microbiology ‘Prof. Paulo de Góes', Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil

Corresponding author: Dr J. F. Siqueira (e-mail: siqueira{at}estacio.br).

Received 22 Feb. 2002; revised version received 10 May 2002; accepted 22 May 2002.

Abstract

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.

This article has been cited by other articles:

				V. Zijnge, G. W. Welling, J. E. Degener, A. J. van Winkelhoff, F. Abbas, and H. J. M. Harmsen Denaturing gradient gel electrophoresis as a diagnostic tool in periodontal microbiology. J. Clin. Microbiol., October 1, 2006; 44(10): 3628 - 3633. [Abstract] [Full Text] [PDF]

				K.-L. Chhour, M. A. Nadkarni, R. Byun, F. E. Martin, N. A. Jacques, and N. Hunter Molecular Analysis of Microbial Diversity in Advanced Caries J. Clin. Microbiol., February 1, 2005; 43(2): 843 - 849. [Abstract] [Full Text] [PDF]