Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, No. 9 Beiguan Street, Tongzhou District, Beijing, 101149, China.
Department of Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.
J Transl Med. 2023 Sep 30;21(1):680. doi: 10.1186/s12967-023-04492-x.
Metagenomic next-generation sequencing (mNGS) has become a powerful tool for pathogen detection, but the value of human sequencing reads generated from it is underestimated.
A total of 138 patients with pleural effusion (PE) were diagnosed with tuberculous pleurisy (TBP, N = 82), malignant pleural effusion (MPE, N = 35), or non-TB infection (N = 21), whose PE samples all underwent mNGS analysis. Clinical TB tests including culture, Acid-Fast Bacillus (AFB) test, Xpert, and T-SPOT, were performed. To utilize mNGS for MPE identification, 25 non-MPE samples (20 TBP and 5 non-TB infection) were randomly selected to set human chromosome copy number baseline and generalized linear modeling was performed using copy number variant (CNV) features of the rest 113 samples (35 MPE and 78 non-MPE).
The performance of TB detection was compared among five methods. T-SPOT demonstrated the highest sensitivity (61% vs. culture 32%, AFB 12%, Xpert 35%, and mNGS 49%) but with the highest false-positive rate (10%) as well. In contrast, mNGS was able to detect TB-genome in nearly half (40/82) of the PE samples from TBP subgroup, with 100% specificity. To evaluate the performance of using CNV features of the human genome for MPE prediction, we performed the leave-one-out cross-validation (LOOCV) in the subcohort excluding the 25 non-MPE samples for setting copy number standards, which demonstrated 54.1% sensitivity, 80.8% specificity, 71.7% accuracy, and an AUC of 0.851.
In summary, we exploited the value of human and non-human sequencing reads generated from mNGS, which showed promising ability in simultaneously detecting TBP and MPE.
宏基因组下一代测序（mNGS）已成为一种强大的病原体检测工具，但人们对其产生的人类测序数据的价值估计不足。
对 138 例胸腔积液（PE）患者进行研究，其中结核性胸膜炎（TBP，N=82）、恶性胸腔积液（MPE，N=35）和非结核感染（N=21），所有患者的胸腔积液样本均进行 mNGS 分析。临床 TB 检测包括培养、抗酸杆菌（AFB）检测、Xpert 和 T-SPOT。为了利用 mNGS 来识别 MPE，随机选择 25 例非 MPE 样本（20 例 TBP 和 5 例非 TB 感染）来设置人类染色体拷贝数基线，并使用其余 113 例样本（35 例 MPE 和 78 例非 MPE）的拷贝数变异（CNV）特征进行广义线性建模。
比较了五种方法检测 TB 的性能。T-SPOT 的敏感性最高（61%比培养 32%、AFB 12%、Xpert 35%和 mNGS 49%），但假阳性率也最高（10%）。相比之下，mNGS 能够检测到近一半（40/82）TBP 亚组 PE 样本中的 TB 基因组，特异性为 100%。为了评估利用人类基因组 CNV 特征预测 MPE 的性能，我们在排除 25 例非 MPE 样本的子队列中进行了留一法交叉验证（LOOCV），以设定拷贝数标准，结果显示敏感性为 54.1%、特异性为 80.8%、准确性为 71.7%、AUC 为 0.851。
总之，我们利用了 mNGS 产生的人类和非人类测序数据的价值，这些数据显示了同时检测 TBP 和 MPE 的有前途的能力。
