The impact of an enhanced infection control protocol on the microbial community profile in molar root canal treatment-an in vivo NGS molecular study

Microbiome analysis in individuals with human papillomavirus oral infection

Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a role in cancer development. We investigated oral microbiome in cancer-free subjects harboring hrHPV oral infection (n = 33) and matched HPV- controls (n = 30). DNA purified from oral rinse-and-gargles of HIV-infected (HIV+) and HIV-uninfected (HIV-) individuals were used for 16S rRNA gene V3-V4 region amplification and sequencing. Analysis of differential microbial abundance and differential pathway abundance was performed, separately for HIV+ and HIV- individuals. Significant differences in alpha (Chao-1 and Shannon indices) and beta diversity (unweighted UniFrac distance) were observed between hrHPV+ and HPV-negative subjects, but only for the HIV- individuals. Infection by hrHPVs was associated with significant changes in the abundance of Saccharibacteria in HIV+ and Gracilibacteria in HIV- subjects. At the genus level, the greatest change in HIV+ individuals was observed for Bulleidia, which was significantly enriched in hrHPV+ subjects. In HIV- individuals, those hrHPV+ showed a significant enrichment of Parvimonas and depletion of Alloscardovia. Our data suggest a possible interplay between hrHPV infection and oral microbiome, which may vary with the HIV status.

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

INTRODUCTION

This study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables.

METHODS

Twenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria.

RESULTS

Of 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree.

CONCLUSIONS

The bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study

AIM

To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform.

METHODOLOGY

Thirty-six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA-like differential expression tool for high-throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2.

RESULTS

The qPCR counts were significantly higher in s1 compared to s2 (p = .0007). The Chao1 index indicated no difference in alpha diversity (p < .7019); whereas Shannon (p = .0056) and Simpson (p = .02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (R2 = .0630, p = .012). Patient ID also showed a significant effect on community composition (R2 = .6961, p = .001). At the genus level, Dialister, Mogibacterium, Prevotella, and Olsenella were differentially enriched at s1, while Actinomyces, Stenotrophomonas_unclassified, Enterococcus_unclassified, and Actinomyces_unclassified were differentially enriched in s2.

CONCLUSION

The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.

The effect of ultrasonic and multisonic irrigation on root canal microbial communities: An ex vivo study

AIM

To analyse the effect of ultrasonic irrigant activation (UIA) and the GentleWave (GW) multisonic irrigation (GW) with minimal instrumentation on the root canal microbial diversity in an ex vivo model that used extracted molars with a history of pulp necrosis.

METHODOLOGY

Twenty-three mandibular molars were prepared ex vivo for collection of superficial (surface control), pre-treatment and post-treatment samples 24 h after extraction. Samples were divided into two groups: UIA using 6% NaOCl (n = 11) and GW group (n = 12). All samples were processed using quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA next-generation sequencing to measure microbial diversity before and after the antimicrobial treatment. For qPCR, a t-test (α = .05) was used to compare the log10 reduction. The Chao1 and Shannon indices evaluated alpha diversity. Differences in community composition (beta diversity) were evaluated by analysis of similarity (ANOSIM). Kruskal-Wallis test with Bonferroni corrections was performed to evaluate the differences in abundances genera in the samples.

RESULTS

Quantitative real-time polymerase chain reaction revealed an estimated 1.6 and 2.6 log10 reduction for UIA and GW groups respectively (p = .048). An average of 5 ± 4 and 3 ± 5 operational taxonomic units (OTUs) were found in surface's samples in the UIA and GW group respectively. These values were significantly lower (p < .001) compared to the number of preoperative OTUs in those groups (155 ± 79 and 187 ± 121). In assessing beta diversity, there were no significant differences found in pre-treatment samples (R = .090, p = .070 ANOSIM with Bonferroni corrections). Also, no significant differences in community composition were observed in post-treatment samples (R = -.05, p = .829). After treatment, there was a significant reduction of Eubacterium using conventional treatment with UIA and a significant reduction of Prevotella using minimal instrumentation with GW irrigation (p = .007 and p = .002 respectively).

CONCLUSION

Quantitative PCR analysis revealed a significant reduction in microbial load for GW group. Overall, diversity changes were similar between UIA and GW irrigation in this ex vivo model that used extracted teeth with a history of pulp necrosis. OTUs obtained from the surface sample were negligible and did not affect the statistical outcome of the study.

Root Canal Dentin Microhardness after Contact with Antibiotic Medications: An In Vitro Study

Background: Antibiotic pastes used as intracanal medication in cases of revascularization therapy might cause negative effects on tooth properties, such as a reduction in dentin microhardness. This in vitro study investigated dentin microhardness in three different locations distancing from the canal lumen after 20 days of treatment with a tri-antibiotic paste (ciprofloxacin, metronidazole, and minocycline), and with a double-antibiotic paste (ciprofloxacin and metronidazole), with calcium hydroxide [Ca(OH)2] UltracalTM XS-treated dentin as comparison. Material and Methods: Human mandibular premolars (n = 48) had the root canals cleaned and shaped and were used to produce dentin slices. Dentin slices remained immersed in the medications for 20 days. The Knoop microhardness (KHN) test was performed before (baseline/Day-0) and after treatment (Day-20) with the medications. Indentations were made at 25 µm, 50 µm, and 100 µm distances from the root canal lumen. The KHN was compared intra-group using Wilcoxon's test. Independent groups were compared using Mann-Whitney's and Kruskal-Wallis' tests, at α = 5%. Results: The microhardness in all the tested groups was reduced at Day-20 in comparison with Day-0 (p < 0.001) (intra-group comparison/same distances). The Day-0 values were similar, and the Day-20 values were higher for the Ca(OH)2 group (p < 0.05) (comparison between groups/same distances). Conclusions: Calcium hydroxide for 20 days would be preferred rather than antibiotic pastes to minimize the expected reduction in dentin microhardness during regenerative procedures.

Effect of different disinfection protocols in bacterial viability of an intraradicular biofilm formed in situ

The present study aimed to evaluate bacterial viability after the use of different disinfection protocols in root canals infected with a multispecies biofilm (MB) formed in situ. Palatal roots with a single canal were obtained from extracted maxillary molars and sterilized before being inserted into the mouth. The roots were contaminated with a MB in an intraoral appliance worn by ten volunteers. All volunteers wore six roots simultaneously in two intraoral devices for 21 days. One root from each volunteer was assigned to each group (n=10): PUI - passive ultrasonic irrigation; EC - Easy Clean; XPF - XP-endo Finisher; aPDT - antimicrobial photodynamic therapy; CI - conventional irrigation; and NC - negative control. The samples were evaluated under confocal laser scanning microscopy. The percentage of viable cells (VC) was calculated over the total percentage of MB biovolume. Data were statistically analyzed (α=5%). The cell viability in the entire root canal or for each third was compared between groups (Kruskal-Wallis test, Dunn post-hoc test) and for the same group (Friedman test, Dunn post-hoc test). Disinfection protocols were not significantly different from each other (P>.05). Samples in EC, PUI, and aPDT had lower cell viability than in NC (P<.05). In the coronal third of samples in the EC, XPF, PUI and aPDT, the percentage of VC biovolume was lower than in the NC (P<.05). The percentage of VC in EC samples was lower in the coronal and middle thirds than in the apical third (P<.05). EC, PUI and aPDT had significant effects on cell viability in intraradicular multispecies biofilm formed in situ when compared with untreated samples.