Application value of targeted next-generation sequencing for identification of non-tuberculous mycobacteria strains

doi:10.19982/j.issn.1000-6621.20220530

Abstract

Abstract:

Objective: To explore the application value of targeted next-generation sequencing (tNGS) in the identification of non-tuberculous mycobacteria (NTM) strains. Methods: From July 2021 to September 2022, 428 samples of hospitalized patients in the NTM Diagnosis and Treatment Center of Guangzhou Chest Hospital were collected for study, including 312 sputum samples and 116 bronchial lavage fluid samples. These samples were identified by tNGS mycobacterium identification (“tNGS” for short) and microbial culture (BACTEC MGIT 960)+DNA microarray chip method (“culture method” for short), and the detection results of the two methods were analyzed. Results: (1) tNGS and culture method respectively isolated 102 and 56 samples of Mycobacterium tuberculosis respectively, and 150 and 182 NTM samples. (2) Detection rate of mycobacterium by tNGS was 58.88% (252/428), but there was no significant difference between tNGS and culture method (55.61% (238/428), χ²=0.936,P=0.333). (3) Taking culture method as the reference standard, the sensitivity, specificity, false negative rate, false positive rate, positive predictive value, negative predictive value and Kappa value of tNGS to detect mycobacterium were 80.65% (200/248), 92.22% (166/180), 22.43% (48/214), 6.54% (14/214), 93.46% (200/214), 77.57% (166/214) and 0.710, respectively. Conclusion: tNGS result is consistent with culture method, has good timeliness, sensitivity and specificity, which is conducive to formulating clinical treatment plan in the early stage.

Key words: Molecular sequence data, Mycobacterium, Diagnosis, differential

CLC Number:

Chen Hua, Chen Pinru, Li Yanyang, Deng Zhengxian, Xu Liuqing, Liang Feng, Hu Jinxing. Application value of targeted next-generation sequencing for identification of non-tuberculous mycobacteria strains[J]. Chinese Journal of Antituberculosis, 2023, 45(4): 362-366. doi: 10.19982/j.issn.1000-6621.20220530

Figures/Tables 2

References 20

[1]	中华医学会结核病学分会. 非结核分枝杆菌病诊断与治疗指南(2020年版). 中华结核和呼吸杂志, 2020, 43(11):918-946. doi:10.3760/cma.j.cn112147-20200508-00570. doi: 10.3760/cma.j.cn112147-20200508-00570
[2]	全国第五次结核病流行病学抽样调查技术指导组, 全国第五次结核病流行病学抽样调查办公室. 2010年全国第五次结核病流行病学抽样调查报告. 中国防痨杂志, 2012, 34(8):485-508.
[3]	全国结核病流行病学抽样调查技术指导组, 全国结核病流行病学抽样调查办公室. 2000年全国结核病流行病学抽样调查报告. 中国防痨杂志, 2002, 24(2):3-46.
[4]	Lee MR, Sheng WH, Hung CC, et al. Mycobacterium abscessus Complex Infections in Humans. Emerg Infect Dis, 2015, 21(9):1638-1646. doi:10.3201/2109.141634. doi: 10.3201/2109.141634
[5]	中华人民共和国国家卫生和计划生育委员会. WS 288—2017肺结核诊断. 2017-11-09.
[6]	中华医学会呼吸病学分会介入呼吸病学学组. 成人诊断性可弯曲支气管镜检查术应用指南(2019年版). 中华结核和呼吸杂志, 2019, 42(8):573-590. doi:10.3760/cma.j.issn.1001-0939.2019.08.005. doi: 10.3760/cma.j.issn.1001-0939.2019.08.005
[7]	Luo F, Darwiche K, Singh S, et al. Performing Bronchoscopy in Times of the COVID-19 Pandemic: Practice Statement from an International Expert Panel. Respiration, 2020, 99(5):417-422. doi:10.1159/000507898. doi: 10.1159/000507898 pmid: 32344422
[8]	田丽丽, 杨新宇, 代小伟, 等. 免疫学检测联合痰涂片和痰培养检测在活动性肺结核临床诊断中的价值. 中国防痨杂志, 2021, 43(10):1073-1078. doi:10.3969/j.issn.1000-6621.2021.10.017. doi: 10.3969/j.issn.1000-6621.2021.10.017
[9]	刘轾彬, 吴敏, 吴小翠, 等. PCR-反向点杂交法检测复治涂阳患者结核分枝杆菌耐药性的价值. 中国防痨杂志, 2021, 43(1):47-51. doi:10.3969/j.issn.1000-6621.2021.01.010. doi: 10.3969/j.issn.1000-6621.2021.01.010
[10]	Li H, Gao H, Meng H, et al. Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing. Front Cell Infect Microbiol, 2018, 8:205. doi:10.3389/fcimb.2018.00205. doi: 10.3389/fcimb.2018.00205 URL
[11]	Shteinberg M, Stein N, Adir Y, et al. Prevalence, risk factors and prognosis of nontuberculous mycobacterial infection among people with bronchiectasis: apopulation survey. Eur Respir J, 2018, 51(5):1702469. doi:10.1183/13993003.02469-2017. doi: 10.1183/13993003.02469-2017
[12]	Li Y, Sun B, Tang X, et al. Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients. Eur J Clin Microbiol Infect Dis, 2020, 39(2):369-374. doi:10.1007/s10096-019-03734-5. doi: 10.1007/s10096-019-03734-5
[13]	陈华, 胡锦兴, 陈品儒, 等. 广州市非结核分枝杆菌流行状况与菌种分布特征:基于2018—2019年数据. 分子影像学杂志, 2021, 44(2):378-382. doi:10.12122/j.issn.1674-4500.2021.02.32. doi: 10.12122/j.issn.1674-4500.2021.02.32
[14]	Johansen MD, Herrmann JL, Kremer L. Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus. Nat Rev Microbiol, 2020, 18(7): 392-407. doi:10.1038/s41579-020-0331-1. doi: 10.1038/s41579-020-0331-1 pmid: 32086501
[15]	中华医学会结核病学分会, 分枝杆菌菌种中文译名原则专家共识编写组. 分枝杆菌菌种中文译名原则专家共识. 中华结核和呼吸杂志, 2018, 41(7): 522-528. doi:10.3760/cma.j.issn.1001-0939.2018.07.003. doi: 10.3760/cma.j.issn.1001-0939.2018.07.003
[16]	van Ingen J, Turenne CY, Tortoli E, et al. A definition of the Mycobacterium avium complex for taxonomical and clinical purposes, a review. Int J Syst Evol Microbiol, 2018, 68(11):3666-3677. doi:10.1099/ijsem.0.003026. doi: 10.1099/ijsem.0.003026 URL
[17]	陈华, 赖晓宇, 陈品儒, 等. 广州地区2018—2021年非结核分枝杆菌临床分离株菌种鉴定结果分析. 实用医学杂志, 2022, 38(17):2191-2197. doi:10.3969/j.issn.1006-5725.2022.17.014. doi: 10.3969/j.issn.1006-5725.2022.17.014
[18]	缪青, 姚雨濛, 潘珏, 等. 宏基因二代测序技术对非结核分枝杆菌感染病原学诊断的价值. 中国临床医学, 2020, 27(4):559-562. doi:10.12025/j.issn.1008-6358.2020.20201289. doi: 10.12025/j.issn.1008-6358.2020.20201289
[19]	孔娇, 陈园园, 蔡青山, 等. 宏基因二代测序技术对非结核分枝杆菌肺病的诊断价值. 中国防痨杂志, 2022, 44(11):1135-1140. doi:10.19982/j.issn.1000-6621.20220298. doi: 10.19982/j.issn.1000-6621.20220298
[20]	Peng JM, Du B, Qin HY, et al. Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients. J Infect, 2021, 82(4):22-27. doi:10.1016/j.jinf.2021.01.029. doi: 10.1016/j.jinf.2021.01.029 URL

菌种	tNGS		培养法
菌种	检出份数	检出率(%)	检出份数	检出率(%)
结核分枝杆菌	102	23.83	56	13.08
非结核分枝杆菌	150	35.05	182	42.52
鸟-胞内分枝杆菌复合群	-	-	46	10.75
鸟分枝杆菌	4	0.93	14	3.27
胞内分枝杆菌	22	5.14	2	0.47
副胞内分枝杆菌	12	2.80	-	-
哥伦比亚分枝杆菌	6	1.40	-	-
蒂莫内分枝杆菌	1	0.23	-	-
罗讷河口分枝杆菌	1	0.23	-	-
奇美拉分枝杆菌	2	0.47	-	-
其他慢生长分枝杆菌
堪萨斯分枝杆菌	-	-	4	0.93
波斯分枝杆菌	2	0.47	-	-
戈登分枝杆菌	4	0.93	-	-
苏尔加分枝杆菌	2	0.47	4	0.93
瘰疬分枝杆菌	4	0.93	-	-
龟-脓肿分枝杆菌复合群	-	-	92	21.50
脓肿分枝杆菌脓肿亚种	62	14.49	-	-
脓肿分枝杆菌马赛亚种	26	6.07	-	-
其他快生长分枝杆菌
偶发分枝杆菌	2	0.47	-	-
冬天分枝杆菌	2	0.47	-	-
无法分辨菌种	8	1.87	20	4.67
阴性	176	41.12	190	44.39

检测方法	MTB阳性		NTM阳性		阴性
检测方法	份数	检出率(%)	份数	检出率(%)	份数	检出率(%)
tNGS	102	23.83	150	35.04	176	41.12
培养法	56	13.08	182	42.52	190	44.39
χ²值	12.019		0.591		0.936^a
P值	0.001		0.442		0.333