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Updated: Sep 19, 2025
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
The presence of Enterococcus in root canal infections based on next-generation sequencing: A systematic review and
Run-Ze Liu1, Li-An Bai1, Yi Luo1
1The State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
Background:
Studies based on next-generation sequencing (NGS) have reported conflicting evidence regarding the presence of Enterococcus in root canal infections.
Objective:
To determine whether Enterococcus prevalence differs among secondary root canal infection (SRCI), persistent root canal infection (PRCI) and primary root canal infection (PrRCI).
Methods:
Literature search was carried out across databases (PubMed, Web of Science, Scopus and Excerpta Medica Database) and other online resources from 1 September 2005, to 24 October 2024. Studies were selected according to inclusion and exclusion criteria. Risk of bias was evaluated according to the JBI Prevalence Critical Appraisal Checklist. The selection of 28 studies focused on the main and secondary outcomes. Pooled estimates of Odds Ratio (OR), prevalence and 95% Confidence Interval (CI) were determined with a common effect or random effects model. Multivariate meta-regression models were fitted. Subgroup analyses were conducted based on sample collection method, region and NGS platform. Sensitivity analysis was conducted to further investigate the robustness of results and to explore plausible causes for heterogeneity.
Results:
Among 28 included studies, 16 studies reporting the detection rate of Enterococcus were incorporated in the meta-analysis. The detection rate of Enterococcus was significantly higher in SRCI than in PrRCI (OR = 2.691; 95% CI: 1.234-5.868; p = .013). The pooled prevalences were 0.400 (95% CI: 0.235-0.565) for SRCI, 0.444 (95% CI: 0.000-0.976) for PRCI and 0.278 (95% CI: 0.087-0.470) for PrRCI, respectively. Within the PrRCI group, the cryogenic pulverization (CP) method yielded a significantly higher detection rate (0.768; 95% CI: 0.642-0.894) than the paper points/hand or rotary instruments (PP) method (0.113; 95% CI: 0.045-0.180). The relative abundance of Enterococcus ranged from 0.01% to 18.88% in SRCI, 2% to 10.5% in PRCI and 0.0008% to 2.03% in PrRCI.
Discussion:
Although a quantitative synthesis of Enterococcus prevalence has been conducted, the data of abundance remain insufficient in literatures.
Conclusion:
A higher prevalence of Enterococcus was correlated with SRCI and PRCI compared to PrRCI. Sample collection method had a significant impact on the prevalence of Enterococcus in the PrRCI context. Enterococcus seems not to be a predominant genus in most studies based on its relatively low abundance.
Registration:
PROSPERO database CRD42024609984.
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