"Checkerboard" versus culture: a comparison between two methods for identification of subgingival microbiota

The present study compared the "checkerboard" DNA-DNA hybridization methodology with culture techniques for the analysis of the composition of the subgingival microbiota. 70 subjects, presenting with a variety of periodontal conditions, contributed with a total of 283 subgingival plaque samples analyzed with respect to the following species: Porphyromonas gingivalis, Prevotella intermedia/Prevotella nigrescens, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, Bacteroides forsythus, Actinobacillus actinomycetemcomitans, Streptococcus sanguis and Streptococcus mutans. Species identification and quantification was performed by (i) the checkerboard method, using whole genomic, digoxigenin labeled DNA probes; and (ii) culture, including non-selective and selective media in combination with routine biochemical testing using commercial test panels. We found that the checkerboard technology resulted in higher prevalence figures for half of the species tested when compared to culture data. If the latter were used as the reference, checkerboard detection sensitivities ranged from 0.17 to 0.86, specificities from 0.17 to 1.0, and diagnostic accuracies from 0.51 to 0.81, depending on bacterial species. The use of the checkerboard data as the reference resulted in detection sensitivities for the culture procedures between 0.24 and 1.0 and specificities between 0.21 and 0.87. The checkerboard methodology resulted in statistically significant higher bacterial counts for the majority of the species. It was further observed that, for most species, the higher the total number colony-forming units in the sample, the higher the discrepancy between the results obtained by the two techniques.