Next-generation metagenome sequencing shows superior diagnostic performance in acid-fast staining sputum smear-negative pulmonary tuberculosis and non-tuberculous mycobacterial pulmonary disease

In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5%, 80.6%, 48.4%, and 32.3%, respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative patients with compromised immune states or poor responses to empirical antibiotics.

本研究旨在探讨下一代宏基因组测序（next-generation metagenome sequencing, mNGS）对於抗酸染色（acid-fast staining, AFS）痰涂片阴性肺结核（pulmonary tuberculosis, PTB）及非结核分枝杆菌肺病（non-tuberculous mycobacterial pulmonary disease, NTM-PD）患者支气管肺泡灌洗液（bronchoalveolar lavage fluid, BALF）样本的临床应用价值。本研究回顾性分析了2018年7月至2021年7月间收治于本院、最终确诊为AFS痰涂片阴性PTB及NTM-PD的肺部感染住院患者的相关数据。从电子病历中提取了支气管镜检查结果，以及mNGS、Xpert、AFS（BALF检测）及血液T-SPOT检测的相关数据。随后比较了上述检测方法针对PTB与NTM-PD的诊断效能。本研究共纳入71例PTB患者与23例NTM-PD患者。针对PTB的诊断，mNGS、Xpert、T-SPOT及AFS的诊断灵敏度分别为94.4%（67/71）、85.9%（61/71）、64.8%（46/71）与28.2%（20/71）；其中mNGS联合Xpert的诊断灵敏度最高，达97.2%（67/71）。Xpert的诊断特异度为100%，AFS与T-SPOT的特异度则分别为73.9%（17/23）与91.3%（21/23）。23例NTM-PD患者的感染均可通过mNGS予以明确鉴定；在免疫功能低下人群亚组中，mNGS、Xpert、T-SPOT及AFS的诊断灵敏度分别为93.5%、80.6%、48.4%与32.3%，其中mNGS联合Xpert的诊断灵敏度最高，达100%（31/31）。该亚组中，Xpert与T-SPOT的特异度均为100%，AFS的特异度则为40%（2/5）。此外，通过mNGS可对所有NTM样本进行精准鉴定。综上，采用mNGS分析BALF样本对结核分枝杆菌（Mycobacterium tuberculosis, MTB）与非结核分枝杆菌（nontuberculous mycobacteria, NTM）的鉴别诊断具有较高准确性；mNGS联合Xpert可提升MTB的检出效能，尤其适用于AFS痰涂片阴性、免疫功能受损或经验性抗生素治疗效果不佳的患者。