Molecular characterization of intact cell-derived and cell-free bacterial DNA from carious dentine samples

Detection of Inflammatory and Homeostasis Biomarkers after Selective Removal of Carious Dentin-An In Vivo Feasibility Study

Deep carious dentin lesions induce an immune reaction within the pulp-dentin complex, leading to the release of cytokines, which might be suitable biomarkers in pulp diagnostics. This in vivo feasibility study determines the concentration of different cytokines after selective removal of carious infected dentin (SCR). In our methodology, paired samples are obtained from 21 patients—each of them with two deep carious lesions at posterior teeth without clinical symptoms. After SCR, lesions are randomly assigned to treatment strategy: Group 1 (11 patients): Carious dentin is covered either with Biodentine^TM (n = 11) or gutta-percha (n = 11) before using the adhesive Optibond^TM FL. Group 2 (10 patients): The adhesives Clearfil^TM SE Protect Bond (n = 10) or Clearfil^TM SE Bond 2 (n = 10) are directly applied. Prepared cavities are rinsed with phosphate buffered saline containing 0.05% Tween 20 (10X) for five minutes immediately after SCR (visit 1) and eight weeks later (visit 2). Rinsing liquid is regained. Concentrations of IL-1β, IL-6, IL-10, C-reactive protein (CRP), TNF-α, IFN-γ, TIMP-1, -2, and MMP-7, -8, -9 are assessed by customized multiplex assays, evaluated with fluorescence analyzer. Non-parametric statistical analysis (Wilcoxon, Mann–Whitney U Test, p < 0.05) is performed (SPSS 25). Our results show that concentrations of CRP, IL-1β, IL-6, TIMP-1, -2, and MMPs were detectable. Median concentrations of CRP, IL-1β und IL-6 were significantly higher in visit 1 (304.9, 107.4, 3.8 pg/mL), compared to visit 2 (67.8, 2.3, 0.0 pg/mL; p_i < 0.001). The study revealed that the non-invasive determination of cytokines from prepared dental cavities is possible.

Antibacterial effect of a brominated self-etch adhesive on carious dentin - An in vivo study

OBJECTIVES

This in vivo study compared the antibacterial effect of a self-etch adhesive with and without the brominated monomer 12-methacryloyloxydodecyl-pyridinium bromide (MDPB) on carious dentin after selective caries removal.

METHODS

10 patients showing deep primary carious lesions at two posterior teeth without pulpal symptoms were included. At visit I, carious tissue was selectively removed and carious dentin was sampled with a sterile roundbur (Komet No. 18). One cavity was restored with composite (SDR, Ceram X; DENTSPLY DeTrey) using an MDPB-containing self-etch adhesive (Clearfil Protect Bond, Kuraray Noritake; PB). The other restoration served as a control (Clearfil SE Bond II, Kuraray Noritake; SE). At visit II after 8 weeks, carious dentin was sampled again. Bacterial growth in carious dentin was differentiated using microbial cultivation. Bacterial DNA from intact cells and cell-free DNA were quantified using 16S rRNA gene-based real-time PCR and the microbial community composition was analyzed by amplicon deep-sequencing. Wilcoxon test was applied for statistical analysis.

RESULTS

Both treatments showed a decrease of intact bacterial cells in carious dentin at visit II compared to visit I (PB: visit I: 1.1*10⁶, visit II: 1.7*10⁵ (p = 0.03); SE: visit I: 1.1*10⁷, visit II = 2.4*10⁵ (p = 0.002)). No statistically significant reduction of cell-free bacterial DNA was detected (PB: visit I: 6.1*10⁵, visit II: 1.6*10⁵ (p = 0.08); SE: visit I: 5.3*10⁵, visit II: 2.9*10⁵ (p = 0.10)). The decrease of intact cell-derived (p = 0.371) and cell-free DNA (p = 0.455) did not differ significantly between PB and SE. Lactobacillus was most abundant within the microbial community at both visits. Alpha-diversity was not affected by treatment and samples showed high intra- and interindividual diversity.

CONCLUSION AND CLINICAL SIGNIFICANCE

Both self-etch adhesives have an antibacterial effect due to a decrease of bacterial DNA after selective caries removal. However, the results do not reveal any additional antibacterial effect by MDPB. The study is registered with the German Clinical Trials Register (DRKS00011532).

Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing

Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA (mcfDNA sequencing) is becoming an attractive diagnostic modality for infectious diseases, allowing broad-range pathogen detection, noninvasive sampling, and rapid diagnosis. At this key juncture in the translation of metagenomics into clinical practice, an integrative perspective is needed to understand the significance of emerging mcfDNA sequencing technology. In this review, we summarized the actual performance of the mcfDNA sequencing tests recently used in health care settings for the diagnosis of a variety of infectious diseases and further focused on the practice considerations (challenges and solutions) for improving the accuracy and clinical relevance of the results produced by this evolving technique. Such knowledge will be helpful for physicians, microbiologists and researchers to understand what is going on in this quickly progressing field of non-invasive pathogen diagnosis by mcfDNA sequencing and promote the routine implementation of this technique in the diagnosis of infectious disease.

Effect of a bioactive cement on the microbial community in carious dentin after selective caries removal - An in-vivo study

OBJECTIVES

Selective caries removal in deep lesions means that soft carious affected dentin is left in the center of the cavity. Thus, using a tricalcium silicate cement Biodentine™ (Septodont, Paris) to seal the remaining soft dentin could have an antibacterial effect. This in-vivo study aimed to do quantitative and qualitative analyses on the bacterial composition within carious dentin before and after selective caries removal when applying Biodentine.

METHODS

Eleven patients with deep primary carious lesions at two posterior teeth without pulpal symptoms were included. Carious dentin was selectively removed and sampled with a sterile round bur (Komet No. 18) at baseline visit and eight weeks later. On the first visit, one lesion per patient, the remaining carious dentin was covered with Biodentine before adhesive restoration. Caries samples were investigated by microbial cultivation, molecular analysis and amplicon deep-sequencing of 16S rRNA genes. Bacterial DNA from intact cells was differentiated from cell-free DNA by DNase degradation prior to DNA isolation.

RESULTS

Reduction of cell-derived as well as cell-free bacterial DNA eight weeks after selective caries removal was significantly higher when Biodentine was applied. Lactobacillus was most abundant within the microbial community of deep carious dentin lesions at the first visit. After intervention with Biodentine application, Lactobacillus was diminished to a high degree. In general, the diversity in samples, as well as bacterial composition differed interindividually as well as intraindividually.

CONCLUSION AND CLINICAL SIGNIFICANCE

Despite the heterogenous and diversity of microbial composition in patients, Biodentine can have beneficial antibacterial effects when applied to residual carious dentin, offering an alternative and safe treatment option. The study is officially registered with German Clinical Trials Register (DRKS00011067).