Comparison between polymerase chain reaction-based and checkerboard DNA hybridization techniques for microbial assessment of subgingival plaque samples

Abstract

Aim: To compare polymerase chain reaction (PCR) with subsequent reverse hybridization (micro-IDent test) and checkerboard DNA–DNA hybridization for the identification of 13 bacterial species in subgingival plaque samples.

Material and Methods: Subgingival plaque samples were taken using paper points and curettes from two sites each with pocket depth <4, 4–6 and >6 mm at baseline and 3 months in 25 periodontitis subjects and two sites in 25 periodontally healthy subjects. Samples were analysed for their content of 13 bacterial species using both assays. Similarities for each species between techniques were determined using regression analysis. Differences between health and periodontitis were determined using the Mann–Whitney test.

Results: Three hundred and fifty samples were evaluated using both techniques. Regression analysis indicated that 10/13 test species showed significant positive correlations between the counts determined by checkerboard analysis and levels determined by the PCR-based test after adjusting for 13 comparisons. The highest rank correlations of 0.58, 0.49 and 0.46 were seen for Treponema denticola, Fusobacterium nucleatum and Eubacterium nodatum, respectively (p<0.0001). Both tests could distinguish samples from healthy and periodontitis subjects.

Conclusion: Detection patterns of 10/13 test species in subgingival plaque samples from periodontitis and healthy subjects were similar using the two molecular techniques.