Nassar Rania, Nassar Mohannad, Mohamed Lobna, Senok Abiola, Williams David
College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK.
Int Endod J. 2025 Jul;58(7):1091-1108. doi: 10.1111/iej.14227. Epub 2025 Mar 26.
The microbiota of endodontic infections in patients from the Arabian Gulf region (AGR) is largely unexplored. While research in different global regions has investigated the microbial composition of such infections, studies using shotgun metagenomic sequencing (SMS) alongside culture-dependent techniques (CDT) are limited. There are also few in vitro biofilm models that reflect the microbial profiles of endodontic infections. Therefore, by employing SMS and CDT, this research aimed to explore compositional and functional microbial profiles of endodontic infections from the AGR. The research also sought to develop ex vivo biofilms directly from endodontic infection samples.
SMS and CDT were used to analyze 32 root canal samples from necrotic pulp. Patients' samples were categorized into two cohorts: symptomatic (n = 19) and asymptomatic (n = 13). Samples underwent sequencing followed by bioinformatic analysis to investigate microbial composition, resistome, virulome, and functional differences. Two representative samples (8R, 15R) were selected to develop ex vivo biofilms on hydroxyapatite coupons. Similarity between inoculum and developed biofilms was assessed using SMS and CDT. The reproducibility of developed biofilms was assessed based on microbial composition and relative abundance at the species level using correlation coefficient analysis.
Endodontic samples had high bacterial diversity, with a total of 366 bacterial species detected across the two cohorts. Several antibiotic resistance (n = 59) and virulence (n = 82) genes were identified, with no significant differences between the cohorts. CDT identified 28 bacterial species, with 71.4% of the isolated bacteria having phenotypic resistance to clinically relevant antibiotics. SMS showed that the ex vivo biofilms were polymicrobial. Biofilm derived from sample 15R had 9 species and was dominated by Enterococcus faecalis, while sample 8R had 12 species and was dominated by Streptococcus mutans. Pearson correlation analysis demonstrated a significant positive correlation between biological biofilm replicates, confirming the reproducibility of biofilm formation.
There was high bacterial diversity in root canal samples from necrotic pulp. Samples were shown to contain antibiotic resistance and virulence genes, with no differences evident between symptomatic and asymptomatic infections. A high number of isolated bacteria were resistant to clinically used antibiotics. Ex vivo biofilm models from clinical samples were successfully developed and reproducibly reflected a polymicrobial composition.
阿拉伯海湾地区（AGR）患者牙髓感染的微生物群在很大程度上尚未得到充分研究。虽然全球不同地区的研究已经调查了此类感染的微生物组成，但同时使用鸟枪法宏基因组测序（SMS）和依赖培养技术（CDT）的研究却很有限。此外，能够反映牙髓感染微生物特征的体外生物膜模型也很少。因此，本研究通过采用SMS和CDT，旨在探索AGR地区牙髓感染的微生物组成和功能特征。该研究还试图直接从牙髓感染样本中构建离体生物膜。
使用SMS和CDT分析32例坏死牙髓的根管样本。患者样本分为两个队列：有症状的（n = 19）和无症状的（n = 13）。样本进行测序，随后进行生物信息学分析，以研究微生物组成、耐药组、毒力组和功能差异。选择两个代表性样本（8R、15R）在羟基磷灰石试片上构建离体生物膜。使用SMS和CDT评估接种物与构建的生物膜之间的相似性。基于微生物组成和物种水平的相对丰度，使用相关系数分析评估构建生物膜的可重复性。
牙髓样本具有高度的细菌多样性，两个队列中共检测到366种细菌。鉴定出了几种抗生素抗性（n = 59）和毒力（n = 82）基因，两个队列之间没有显著差异。CDT鉴定出28种细菌，71.4%的分离细菌对临床相关抗生素具有表型抗性。SMS显示离体生物膜是多微生物的。源自样本15R的生物膜有9种细菌，以粪肠球菌为主，而样本8R有12种细菌，以变形链球菌为主。Pearson相关分析表明生物膜复制品之间存在显著正相关，证实了生物膜形成的可重复性。
坏死牙髓的根管样本中细菌多样性高。样本显示含有抗生素抗性和毒力基因，有症状和无症状感染之间没有明显差异。大量分离细菌对临床使用的抗生素具有抗性。成功构建了来自临床样本的离体生物膜模型，可重复地反映了多微生物组成。
