The mNGS result of the first BALF sample (the second day) and the second BALF sample (the ninth day).

The patient we reported was finally diagnosed with endobronchial tuberculosis after two mNGS  of BALF, narrowing of the opening of the left upper lobe bronchusand under fiberoptic bronchoscope and chest CT scans. BALF specimen was directly sent to Clinical Genome Center, Guangxi Kingmed Diagnostics, for mNGS via Illumina platform. The methods of mNGS were the same as that described in previously published mNGS articles(1, 2). The mNGS result of the first BALF  indicated 1091, 267 and one sequence readings of Haemophilus influenzae, Streptococcus pneumoniae and MTB, with coverage of 11.16%, 2.45%, 0.001577% respectively.  And two sequences of MTB were detected by the mNGS of the second BALF with a coverage of <0.01%.

1.Shi Y, Chen J, Shi X, Hu J, Li H, Li X, et al. A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review. BMC infectious diseases. 2021; 21:621.

2. Qin Z, Zou Y, Huang Z, Yu N, Deng Z, Chen Z, et al. Metagenomic next-generation sequencing contributes to the diagnosis of mixed pulmonary infection: a case report. Annals of clinical microbiology and antimicrobials. 2022; 21:52.

本报告所涉患者经两次支气管肺泡灌洗液（bronchoalveolar lavage fluid, BALF）宏基因组二代测序（metagenomic next-generation sequencing, mNGS）、纤维支气管镜下左上叶支气管开口狭窄表现及胸部CT扫描，最终确诊为支气管内膜结核。
支气管肺泡灌洗液标本直接送检至广西金域诊断临床基因组中心，通过Illumina平台开展宏基因组二代测序检测。本次检测所采用的mNGS方法与既往发表的相关文献（1, 2）所述一致。
首次支气管肺泡灌洗液的mNGS结果显示：流感嗜血杆菌、肺炎链球菌及结核分枝杆菌（Mycobacterium tuberculosis, MTB）的序列读长分别为1091、267和1条，覆盖度分别为11.16%、2.45%、0.001577%。第二次支气管肺泡灌洗液的mNGS检测到2条MTB序列，覆盖度<0.01%。

1. Shi Y, Chen J, Shi X, Hu J, Li H, Li X, et al. 宏基因组二代测序诊断鹦鹉热衣原体致重症肺炎合并脑膜炎一例并临床分析：病例报告及文献复习. BMC传染病. 2021; 21:621.
2. Qin Z, Zou Y, Huang Z, Yu N, Deng Z, Chen Z, et al. 宏基因组二代测序助力混合肺部感染诊断：一例病例报告. 临床微生物学与抗菌药物年鉴. 2022; 21:52.