Background: The aim of this study was to identify a sampling strategy with high probability for detecting oral colonization by Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Eikenella corrodens, Tannerella forsythensis, Prevotella intermedia, Prevotella nigrescens, and Treponema denticola before and following mechanical periodontal therapy.

Methods: Samples were taken from the following intraoral sites in 35 patients with untreated chronic periodontitis before and 1.5, 3, and 6 months after non-surgical periodontal therapy: supra- and subgingival plaque from the deepest pockets in each sextant; pooled supra- and subgingival plaque from another six randomly selected, less affected teeth; mucosal swab samples from the tongue, tonsils, throat, and buccal mucosa; and stimulated and unstimulated saliva. Microbial species were identified by polymerase chain reaction (PCR).

Results: Of the sampling of all assessed sites, the highest probability for simultaneously detecting the tested pathogens was found in respect to the combination of supra- and subgingival plaque samples taken from the most affected tooth in each sextant in untreated patients (probability: 83% to 95% for the assessed bacteria). These results were consistently observed throughout the study period.

Conclusions: For determining the intraoral carrier state of patients with periodontitis, a combined sample of supra- and subgingival plaque taken from the deepest periodontal pocket in each sextant may yield the most reliable result. This sampling strategy may be used in routine microbial testing and clinical research.