Assessing next-generation sequencing for Mycobacterium tuberculosis diagnosis in clinical sputum samples

doi:10.19982/j.issn.1000-6621.20220097

Abstract

Abstract:

Objective: To evaluate detection efficacy of next-generation sequencing (NGS) to Mycobacterium tuberculosis from clinical sputum samples. Methods: Sputum samples of 49 suspected pulmonary tuberculosis patients diagnosed in Tuberculosis Outpatient Department of Beijing Center for Disease Prevention and Control (Beijing Center for Tuberculosis Research and Control) were collected from August to November, 2021. Suspected pulmonary tuberculosis were detected from sputum samples with acid-fast staining (smear),L-J culture and MGIT 960 liquid culture (culture), GeneXpert MTB/RIF (Xpert) and NGS methods. The positive detection rates of 4 kinds of methods were compared in the selected patients. We also evaluated the detection efficacy of different methods based on the results of clinical diagnosis. Results: There were 40 pulmonary tuberculosis patients (25 confirmed pathogen-positive pulmonary tuberculosis patients and 15 clinical diagnosed cases) and 9 non-pulmonary tuberculosis patients (6 cases of pneumonia, 1 case of nontuberculous mycobacteria infection, 1 case of COPD and 1 case of asthma). The positive detection rates are statistically difference (χ²=17.614,17.018,20.753;Ps=0.000) among smear 44.9% (22/49), culture 51.0% (25/49), Xpert 49.0% (24/49) and NGS 69.4% (34/49). For etiology-negative pulmonary tuberculosis patients, the positive detection rate by the NGS was 46.7% (7/15). Sensitivity were 55.0% (22/40), 60.0% (24/40), 60.0% (24/40), 80.0% (32/40), and specificity were 9/9, 8/9, 9/9, 7/9, and concordance rate were 63.3% (31/49), 65.3% (32/49), 67.3% (33/49), 79.6% (39/49), Kappa values were 0.310,0.297,0.355,0.459 based on smear, culture, Xpert and NGS respectively. Conclusion: NGS has the highest sensitivity and consistency based on the national clinical diagnosis standard of pulmonary tuberculosis, which can diagnose suspected pulmonary tuberculosis earlier and detect Mycobacterium tuberculosis from sputum samples rapidly and effectively.

Key words: Mycobacterium tuberculosis, Diagnostic techniques and procedures, Comparative study

DAI Xiao-wei, WANG Nen-han, CHEN Shuang-shuang, YANG Xin-yu, TIAN Li-li, CHEN Hong, ZHANG Hong-tai, LI Chuan-you. Assessing next-generation sequencing for Mycobacterium tuberculosis diagnosis in clinical sputum samples[J]. Chinese Journal of Antituberculosis, 2022, 44(7): 669-679. doi: 10.19982/j.issn.1000-6621.20220097

Figures/Tables 3

References 22

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患者分类	总例数	涂片[例(阳性率,%)]	培养[例(阳性率,%)]	Xpert[例(阳性率,%)]	NGS[例(阳性率,%)]	χ²值	P值
肺结核	40	22(44.9)	24(49.0)	24(49.0)	32(65.3)	6.383	0.094
病原学阳性确诊	25	22(88.0)	24(96.0)	24(96.0)	25(100.0)	4.000	0.261
病原学阴性临床诊断	15	0(0.0)	0(0.0)	0(0.0)	7(46.7)	23.774	0.000
非肺结核	9	0(0.0)	1(11.1)	0(0.0)	2(22.2)	4.000	0.261
肺炎	6	0(0.0)	0(0.0)	0(0.0)	1(16.7)	-	-
非结核分枝杆菌病	1	0(0.0)	1(100.0)	0(0.0)	0(0.0)	-	-
慢性阻塞性肺疾病	1	0(0.0)	0(0.0)	0(0.0)	1(16.7)	-	-
哮喘	1	0(0.0)	0(0.0)	0(0.0)	0(0.0)	-	-