Song Tiange, Yin Lin, Zhou Xiaoli, Tao Xiaoyan, Tie Dandan, Zhang Jie, Jiang Li
Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
Front Cell Infect Microbiol. 2025 May 8;15:1567981. doi: 10.3389/fcimb.2025.1567981. eCollection 2025.
Infectious diseases that require tissue biopsy are usually more difficult to diagnose through conventional microbiological tests (CMT), and knowledge of the infection microbiota pattern from biopsied tissues remains incomplete. Our study aimed to investigate the diagnostic and prognostic value of metagenomic next-generation sequencing (mNGS), characterize the microbiota profile from biopsied tissues, and examine its relationship with clinical outcomes.
This retrospective cohort study included 110 patients who underwent tissue biopsy and sent both mNGS and CMT due to suspected complex infection. Microbiota patterns were illustrated via unsupervised hierarchical clustering analysis. Multivariate regression analysis was used to investigate the effect measures.
The sensitivity of mNGS was significantly higher than that of CMT regarding bacteria (87.23% 40.43%, P=0.01), viruses (100% 5.56%, P<0.001), and fungi (87.5% 28.6%, P=0.04). Polymicrobial infection accounted for 45.2% (33/73) of the infection samples. In skeletal articular biopsied tissues, Staphylococcus presented the highest mean abundance among different species of bacteria (21.2% of all bacterial reads, standard deviation (SD) 38.9). Anaerobic bacteria (24.0%, SD 25.9) represented the most common bacteria in biopsied tissue from the lung or mediastinum. The presence of gram-negative bacteria (adjusted OR 5.21, 95% CI 1.39-19.43, P=0.01), Enterobacteriaceae (adjusted OR 5.71, 95% CI 1.17-28.03, P=0.03) and Staphylococcus (adjusted OR 8.64, 95% CI 1.95-38.34, P=0.005) was associated with an increased risk of treatment failure. Early mNGS sampling within 7 days after admission was associated with a significantly decreased risk of all-cause mortality (HR 0.18, 95% CI 0.04-0.94; P=0.04), treatment failure (OR 0.17, 95% CI 0.05-0.66; P=0.01), and increased probability of clinical resolution (OR 3.03, 95% CI 1.24-7.40; P=0.01).
mNGS demonstrates significant diagnostic and prognostic efficacy in patients undergoing tissue biopsy for suspected complex infections. The presence of Gram-negative bacteria, Enterobacteriaceae, and Staphylococcus is associated with a higher probability of treatment failure, which underscores the advantage of using mNGS to guide more aggressive antibiotic strategies.
需要组织活检的感染性疾病通常通过传统微生物检测（CMT）更难诊断，并且来自活检组织的感染微生物群模式的相关知识仍不完整。我们的研究旨在调查宏基因组下一代测序（mNGS）的诊断和预后价值，描绘活检组织中的微生物群特征，并检查其与临床结果的关系。
这项回顾性队列研究纳入了110例因疑似复杂感染而接受组织活检并同时进行mNGS和CMT检测的患者。通过无监督层次聚类分析展示微生物群模式。使用多变量回归分析来研究效应指标。
在细菌（87.23%对40.43%，P = 0.01）、病毒（100%对5.56%，P < 0.001）和真菌（87.5%对28.6%，P = 0.04）方面，mNGS的敏感性显著高于CMT。混合微生物感染占感染样本的45.2%（33/73）。在骨骼关节活检组织中，葡萄球菌在不同细菌种类中平均丰度最高（占所有细菌读数的21.2%，标准差（SD）38.9）。厌氧菌（24.0%，SD 25.9）是肺或纵隔活检组织中最常见的细菌。革兰氏阴性菌（校正OR 5.21，95%CI 1.39 - 19.43，P = 0.01）、肠杆菌科（校正OR 5.71，95%CI 1.17 - 28.03，P = 0.03）和葡萄球菌（校正OR 8.64，95%CI 1.95 - 38.34，P = 0.005）的存在与治疗失败风险增加相关。入院后7天内尽早进行mNGS采样与全因死亡率显著降低（HR 0.18，95%CI 0.
