宏基因组二代测序在疑难感染性疾病中的临床应用价值

韩思雨

doi:10.7499/j.issn.1008-8830.2110064

PDF(515 KB)

HTML

中国当代儿科杂志 ›› 2022, Vol. 24 ›› Issue (2) : 210-215. DOI: 10.7499/j.issn.1008-8830.2110064

综述

宏基因组二代测序在疑难感染性疾病中的临床应用价值

韩思雨

作者信息 +

Clinical value of metagenomic next-generation sequencing in complicated infectious diseases

HAN Si-Yu

Author information +

文章历史 +

摘要

感染性疾病是临床常见疾病，病原体诊断是其诊治中的关键环节。而常规病原体检测方法耗时长、阳性率低，难以满足临床需求，宏基因组二代测序（metagenomic next-generation sequencing，mNGS）作为一种新型病原检测方法，检测范围广泛，可检测细菌、病毒、真菌、寄生虫、罕见病原体、甚至未知病原体。mNGS具有无偏倚性，可以快速、高效、准确获得检测样本中所有核酸信息，分析出致病病原体，指导临床诊断和治疗，在疑难感染性疾病中发挥着重要作用。该文综述mNGS在细菌、真菌、病毒、寄生虫等感染中的诊断优势和临床应用价值。

Abstract

Infectious diseases are commonly seen in clinical practice, and pathogen diagnosis is the key link in diagnosis and treatment; however, conventional pathogen detection methods cannot meet clinical needs due to time-consuming operation and low positive rate. As a new pathogen detection method, metagenomic next-generation sequencing (mNGS) has a wide detection range and can detect bacteria, viruses, fungi, parasites, rare pathogens, and even unknown pathogens. The technique of mNGS is unbiased and can rapidly, efficiently, and accurately obtain all nucleic acid information in test samples, analyze pathogens, and guide clinical diagnosis and treatment, thereby playing an important role in complicated infectious diseases. This article reviews the diagnostic advantages and clinical value of mNGS in bacterial, fungal, viral, and parasitic infections.

导出引用

韩思雨. 宏基因组二代测序在疑难感染性疾病中的临床应用价值[J]. 中国当代儿科杂志. 2022, 24(2): 210-215 https://doi.org/10.7499/j.issn.1008-8830.2110064

HAN Si-Yu. Clinical value of metagenomic next-generation sequencing in complicated infectious diseases[J]. Chinese Journal of Contemporary Pediatrics. 2022, 24(2): 210-215 https://doi.org/10.7499/j.issn.1008-8830.2110064

参考文献

1 Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases[J]. Clin Infect Dis, 2018, 66(5): 778-788. PMID: 29040428. PMCID: PMC7108102. DOI: 10.1093/cid/cix881.
2 Zhang XX, Guo LY, Liu LL, et al. The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis[J]. BMC Infect Dis, 2019, 19(1): 495. PMID: 31164085. PMCID: PMC6549306. DOI: 10.1186/s12879-019-4132-y.
3 Huang J, Jiang EL, Yang DL, et al. Metagenomic next-generation sequencing versus traditional pathogen detection in the diagnosis of peripheral pulmonary infectious lesions[J]. Infect Drug Resist, 2020, 13: 567-576. PMID: 32110067. PMCID: PMC7036976. DOI: 10.2147/IDR.S235182.
4 Xie Y, Du J, Jin W, et al. Next generation sequencing for diagnosis of severe pneumonia: China, 2010-2018[J]. J Infect, 2019, 78(2): 158-169. PMID: 30237069. DOI: 10.1016/j.jinf.2018.09.004.
5 Pan L, Pan XH, Xu JK, et al. Misdiagnosed tuberculosis being corrected as Nocardia farcinica infection by metagenomic sequencing: a case report[J]. BMC Infect Dis, 2021, 21(1): 754. PMID: 34348670. PMCID: PMC8335456. DOI: 10.1186/s12879-021-06436-6.
6 中华医学会结核病学分会, 结核病病理学诊断专家共识编写组. 中国结核病病理学诊断专家共识[J]. 中华结核和呼吸杂志, 2017, 40(6): 419-425. DOI: 10.3760/cma.j.issn.1001-0939.2017.06.005.
7 Zellweger JP, Sotgiu G, Block M, et al. Risk assessment of tuberculosis in contacts by IFN-γ release assays. A Tuberculosis Network European Trials Group study[J]. Am J Respir Crit Care Med, 2015, 191(10): 1176-1184. PMID: 25763458. DOI: 10.1164/rccm.201502-0232OC.
8 Jin WT, Pan J, Miao Q, et al. Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital[J]. Ann Transl Med, 2020, 8(17): 1065. PMID: 33145284. PMCID: PMC7575944. DOI: 10.21037/atm-20-2274.
9 Wang SN, Chen YL, Wang DM, et al. The feasibility of metagenomic next-generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid[J]. Front Microbiol, 2019, 10: 1993. PMID: 31551954. PMCID: PMC6733977. DOI: 10.3389/fmicb.2019.01993.
10 Shi CL, Han P, Tang PJ, et al. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis[J]. J Infect, 2020, 81(4): 567-574. PMID: 32768450. DOI: 10.1016/j.jinf.2020.08.004.
11 戴媛媛, 马筱玲. 宏基因组二代测序技术在临床病原学诊断中的应用[J]. 临床检验杂志, 2021, 39(1): 1-5. DOI: 10.13602/j.cnki.jcls.2021.01.01.
12 林爱清, 张璐, 成宝涛, 等. 二代测序技术应用于脑脊液检测在结核性脑膜炎中的早期诊断价值[J]. 中华实验和临床感染病杂志(电子版), 2020, 14(4): 291-295. DOI: 10.3877/cma.j.issn.1674-1358.2020.04.005.
13 《中华传染病杂志》编辑委员会. 中国宏基因组学第二代测序技术检测感染病原体的临床应用专家共识[J]. 中华传染病杂志, 2020, 38(11): 681-689. DOI: 10.3760/cma.j.cn311365-20200731-00732.
14 夏云, 杜丽, 何云燕. 侵袭性曲霉病实验室诊断的现状和展望[J]. 中华检验医学杂志, 2018, 41(1): 9-12. DOI: 10.3760/cma.j.issn.1009-9158.2018.01.003.
15 贾建超, 贾建敏, 刘姿, 等. 宏基因组学二代测序技术对重症肺炎真菌感染诊断价值[J]. 中华实用诊断与治疗杂志, 2020, 34(10): 1023-1025. DOI: 10.13507/j.issn.1674-3474.2020.10.014.
16 He BC, Liu LL, Chen BL, et al. The application of next-generation sequencing in diagnosing invasive pulmonary aspergillosis: three case reports[J]. Am J Transl Res, 2019, 11(4): 2532-2539. PMID: 31105860 PMCID:PMC6511794.
17 Wilson MR, O'Donovan BD, Gelfand JM, et al. Chronic meningitis investigated via metagenomic next-generation sequencing[J]. JAMA Neurol, 2018, 75(8): 947-955. PMID: 29710329. PMCID: PMC5933460. DOI: 10.1001/jamaneurol.2018.0463.
18 葛瑛, 范思远, 陈健华, 等. 隐球菌脑膜炎患者脑脊液宏基因组二代测序结果分析[J]. 协和医学杂志, 2019, 10(6): 605-611. DOI: 10.3969/j.issn.1674-9081.2019.06.010.
19 费笑非, 杜芳, 张红鸭, 等. 隐球菌性脑膜炎不同检测方法诊断价值比较[J]. 疑难病杂志, 2020, 19(6): 582-586. DOI: 10.3969/j.issn.1671-6450.2020.06.011.
20 Ji XC, Zhou LF, Li CY, et al. Reduction of human DNA contamination in clinical cerebrospinal fluid specimens improves the sensitivity of metagenomic next-generation sequencing[J]. J Mol Neurosci, 2020, 70(5): 659-666. PMID: 32002752. DOI: 10.1007/s12031-019-01472-z.
21 Jerome H, Taylor C, Sreenu VB, et al. Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers[J]. J Infect, 2019, 79(4): 383-388. PMID: 31398374. PMCID: PMC6859916. DOI: 10.1016/j.jinf.2019.08.003.
22 Carpenter ML, Tan SK, Watson T, et al. Metagenomic next-generation sequencing for identification and quantitation of transplant-related DNA viruses[J]. J Clin Microbiol, 2019, 57(12): e01113-19. PMID: 31554674. PMCID: PMC6879295. DOI: 10.1128/JCM.01113-19.
23 刘龙群, 吴可人, 杨艳, 等. 基因二代测序检测登革热1例[J]. 临床肺科杂志, 2020, 25(11): 1776-1777. DOI: 10.3969/j.issn.1009-6663.2020.11.037.
24 Wilson MR, Sample HA, Zorn KC, et al. Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis[J]. N Engl J Med, 2019, 380(24): 2327-2340. PMID: 31189036. PMCID: PMC6764751. DOI: 10.1056/NEJMoa1803396.
25 顾鹏, 许书添, 姜雪, 等. 外周血宏基因组二代测序对肺孢子菌肺炎的诊断价值[J]. 肾脏病与透析肾移植杂志, 2020, 29(1): 8-13. DOI: 10.3969/j.issn.1006-298X.2020.01.002.
26 Wu XD, Li YY, Zhang M, et al. Etiology of severe community-acquired pneumonia in adults based on metagenomic next-generation sequencing: a prospective multicenter study[J]. Infect Dis Ther, 2020, 9(4): 1003-1015. PMID: 33170499. PMCID: PMC7652912. DOI: 10.1007/s40121-020-00353-y.
27 Xiao W, Han P, Xu ZJ, et al. Pulmonary scedosporiosis in a patient with acute hematopoietic failure: diagnosis aided by next-generation sequencing[J]. Int J Infect Dis, 2019, 85: 114-116. PMID: 31170547. DOI: 10.1016/j.ijid.2019.05.033.
28 杜秀芳, 罗凤鸣. 二代基因测序技术确诊嗜肺军团菌肺炎一例[J]. 中国呼吸与危重监护杂志, 2020, 19(5): 507-509. DOI: 10.7507/1671-6205.202001027.
29 Huang YN, Ma YY, Miao Q, et al. Arthritis caused by Legionella micdadei and Staphylococcus aureus: metagenomic next-generation sequencing provides a rapid and accurate access to diagnosis and surveillance[J]. Ann Transl Med, 2019, 7(20): 589. PMID: 31807570. PMCID: PMC6861802. DOI: 10.21037/atm.2019.09.81.
30 Gu L, Liu W, Ru M, et al. The application of metagenomic next-generation sequencing in diagnosing Chlamydia psittaci pneumonia: a report of five cases[J]. BMC Pulm Med, 2020, 20(1): 65. PMID: 32178660. PMCID: PMC7077129. DOI: 10.1186/s12890-020-1098-x.
31 Chen XC, Cao K, Wei Y, et al. Metagenomic next-generation sequencing in the diagnosis of severe pneumonias caused by Chlamydia psittaci[J]. Infection, 2020, 48(4): 535-542. PMID: 32314307. PMCID: PMC7223968. DOI: 10.1007/s15010-020-01429-0.
32 Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing[J]. N Engl J Med, 2014, 370(25): 2408-2417. PMID: 24896819. PMCID: PMC4134948. DOI: 10.1056/NEJMoa1401268.
33 Zhang P, Chen Y, Li SY, et al. Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study[J]. PeerJ, 2020, 8: e9623. PMID: 32821543. PMCID: PMC7395598. DOI: 10.7717/peerj.9623.