邮件订阅 RSS

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

宏基因组高通量测序技术的临床应用：现状、挑战与前景

刁振丽,  李金明

downloadPDF
文章导航 > 协和医学杂志  > 2023 > 优先出版
刁振丽, 李金明. 宏基因组高通量测序技术的临床应用：现状、挑战与前景[J]. 协和医学杂志. doi: 10.12290/xhyxzz.2023-0089
引用本文: 刁振丽, 李金明. 宏基因组高通量测序技术的临床应用：现状、挑战与前景[J]. 协和医学杂志. doi: 10.12290/xhyxzz.2023-0089
shu
DIAO Zhenli, LI Jinming. Current Status, Challenges and Prospects of Clinical Application for Metagenomic Next Generation Sequencing[J]. Medical Journal of Peking Union Medical College Hospital. doi: 10.12290/xhyxzz.2023-0089
Citation: DIAO Zhenli, LI Jinming. Current Status, Challenges and Prospects of Clinical Application for Metagenomic Next Generation Sequencing[J]. Medical Journal of Peking Union Medical College Hospital. doi: 10.12290/xhyxzz.2023-0089
shu

宏基因组高通量测序技术的临床应用：现状、挑战与前景

doi: 10.12290/xhyxzz.2023-0089

  • 1 北京医院/国家老年医学中心 国家卫生健康委临床检验中心中国医学科学院老年医学研究院, 北京 100730;

  • 2 国家卫生健康委临床检验中心/北京协和医学院/中国医学科学院, 北京 100730

详细信息
    通讯作者:

    李金明,E-mail:jmli@nccl.org.cn

  • 中图分类号: R446.5;R51

Current Status, Challenges and Prospects of Clinical Application for Metagenomic Next Generation Sequencing

  • 1 National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing 100730, China;

  • 2 National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China

    摘要
  • 摘要: 传统的微生物学检测方法难以满足临床上复杂多变的病原体检测需求。近年来，新兴的宏基因组高通量测序（ metagenomic next generation sequencing,mNGS）技术被广泛应用于各种感染性疾病诊断、新发突发传染病病因分析、耐药基因检测和宿主免疫应答分析等领域。 mNGS 检测流程十分复杂，检测过程中每一步骤引入的变异均会影响检测结果的准确性。检测方法缺乏标准化、人员认知和能力不足、仪器试剂成本高昂是 mNGS 临床推广面临的主要障碍。检测方法的标准化、规范化，人员知识和能力的提升是目前 mNGS 检测面临的迫切需求。整合 mNGS 病原体信息、转录组信息和耐药基因信息以综合提高感染性疾病患者的临床管理水平是 mNGS 检测的重要发展方向。
    Abstract: Traditional microbial detection methods have difficulty meeting the needs of pathogen detection in the clinic. In recent years, metagenomic next-generation sequencing (mNGS) technology has emerged and been widely used in the diagnosis of various infectious diseases, the etiological analysis of emerging infectious diseases, the detection of drug resistance genes and the analysis of the host immune response. The mNGS workflow is complicated, and the variation introduced in each step will influence the accuracy of the detection results. The absence of standardized methods, the lack of personnel knowledge and ability, and the expensive cost of instruments and reagents are the main obstacles to the clinical application of mNGS. The standardization and normalization of methods as well as the improvement of personnel knowledge and ability are currently urgently needed for mNGS detection. The integration of pathogen, transcriptome and antibiotic resistance genes information to comprehensively improve the clinical management level of patients with infectious diseases is an important direction of mNGS detection.
    • HTML全文
    • 参考文献(34)
  • [1] Marais G, Hardie D, Brink A. A case for investment in clinical metagenomics in low-income and middle-income countries[J]. Lancet Microbe, 2023, 4:e192-e199.
    [2] 韩东升, 马筱玲, 吴文娟. 病原体宏基因组高通量测序医院实验室本地化之路:现状和挑战[J]. 中华检验医学杂志, 2022,45:100-104.
    [3] Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet,2019,20:341-355.
    [4] Han D, Diao Z, Lai H, et al. Multilaboratory assessment of metagenomic nextgeneration sequencing for unbiased microbe detection[J]. J Adv Res, 2022,38:213-222.
    [5] Miller S, Naccache SN, Samayoa E, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid[J]. Genome Res, 2019,29:831-842.
    [6] Wilson MR, Sample HA, Zorn KC, et al. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis[J]. N Engl J Med, 2019,380:2327-2340.
    [7] Diao Z, Lai H, Han D, et al. Validation of a Metagenomic Next-Generation Sequencing Assay for Lower Respiratory Pathogen Detection[J]. Microbiol Spectr, 2022:e0381222.
    [8] Diao Z, Han D, Zhang R, et al. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections[J]. J Adv Res, 2022,38:201-212.
    [9] Chien JY, Yu CJ, Hsueh PR. Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units[J]. Microbiol Spectr, 2022,10:e0074622.
    [10] Blauwkamp TA, Thair S, Rosen MJ, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease[J]. Nat Microbiol, 2019,4:663-674.
    [11] Velmurugan G, Dinakaran V, Rajendhran J, et al. Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease[J]. Trends Endocrinol Metab, 2020,31:835-847.
    [12] 陶悦, 傅启华, 莫茜. 病原宏基因组测序在新型冠状病毒检测中的应用与挑战[J]. 中华检验医学杂志, 2020,43:217-220.
    [13] Lin B, Hui J, Mao H. Nanopore Technology and Its Applications in Gene Sequencing[J]. Biosensors (Basel), 2021,11:214.
    [14] Boolchandani M, D'Souza A W, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance[J]. Nat Rev Genet, 2019,20:356-370.
    [15] Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection[J]. Nat Biotechnol, 2019,37:783-792.
    [16] Serpa PH, Deng X, Abdelghany M, et al. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections[J]. Genome Med, 2022,14:74.
    [17] 中华医学会检验医学分会临床微生物学组, 中华医学会微生物学与免疫学分会临床微生物学组, 中国医疗保健国际交流促进会临床微生物与感染分会. 宏基因组高通量测序技术应用于感染性疾病病原检测中国专家共识[J]. 中华检验医学杂志, 2021,44:107-120.
    [18] Langelier C, Kalantar KL, Moazed F, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults[J]. Proc Natl Acad Sci U S A, 2018,115:e12353-e12362.
    [19] Kalantar K L, Neyton L, Abdelghany M, et al. Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults[J]. Nat Microbiol, 2022,7:1805-1816.
    [20] Ramachandran PS, Ramesh A, Creswell FV, et al. Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics[J]. Nat Commun, 2022,13:1675.
    [21] Han D, Li Z, Li R, et al. mNGS in clinical microbiology laboratories:on the road to maturity[J]. Crit Rev Microbiol, 2019,45:668-685.
    [22] Di H, Thor SW, Trujillo AA, et al. Comparison of nucleic acid extraction methods for next-generation sequencing of avian influenza A virus from ferret respiratory samples[J]. J Virol Methods, 2019,270:95-105.
    [23] Gryp T, Glorieux G, Joossens M, et al. Comparison of five assays for DNA extraction from bacterial cells in human faecal samples[J]. J Appl Microbiol, 2020,129:378-388.
    [24] Scharf S, Bartels A, Kondakci M, et al. Introduction of a bead beating step improves fungal DNA extraction from selected patient specimens[J]. Int J Med Microbiol, 2020,310:151443.
    [25] Hasan MR, Rawat A, Tang P, et al. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by NextGeneration Sequencing[J]. J Clin Microbiol, 2016,54:919-927.
    [26] Lopez-Labrador FX, Brown JR, Fischer N, et al. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I:Wet lab procedure[J]. J Clin Virol, 2021,134:104691.
    [27] Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections[J]. J Adv Res 2022,38:201-212.
    [28] Grumaz S, Stevens P, Grumaz C, et al. Next-generation sequencing diagnostics of bacteremia in septic patients[J]. Genome Med, 2016,8:73.
    [29] 中华医学会检验医学分会. 高通量宏基因组测序技术检测病原微生物的临床应用规范化专家共识[J]. 中华检验医学杂志, 2020,43:1181-1195.
    [30] Liu D, Zhou H, Xu T, et al. Multicenter assessment of shotgun metagenomics for pathogen detection[J]. EBioMedicine, 2021,74:103649.
    [31] 中华医学会检验医学分会. 宏基因组测序病原微生物检测生物信息学分析规范化管理专家共识[J]. 中华检验医学杂志, 2021,44:799-807.
    [32] de Vries J J C, Brown J R, Couto N, et al. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting[J]. J Clin Virol, 2021, 138:104812.
    [33] Wilson MR, O'Donovan BD, Gelfand JM, et al. Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing[J]. JAMA Neurol, 2018,75:947-955.
    [34] Miao Q, Ma Y, Wang Q, et al. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice[J]. Clin Infect Dis, 2018,67:s231-s240.
    • 相关文章
    • 施引文献
  • 资源附件(0)
  • 加载中
WeChat 点击查看大图
计量
  • 文章访问数:  114
  • HTML全文浏览量:  19
  • PDF下载量:  34
  • 被引次数: 0
出版历程
  • 收稿日期:  2023-02-17
  • 录用日期:  2023-03-20
  • 网络出版日期:  2023-03-30

目录

    /

    返回文章
    返回
    友情链接: 国家卫生健康委员会 北京协和医院 中国医学科学院 学术不端检测系统 国际知识资源总库 中国知网 术语在线 中国全科医学
    地址：北京市东城区帅府园1号 北京协和医院老楼7号楼
    3层302室 《协和医学杂志》编辑部
    电话：010-69154261/4262
    E - mail：medj@pumch.cn
    mjpumch@126.com
    期刊网站版权所有：《协和医学杂志》编辑部
    京ICP备 11002662

    本系统由 北京仁和汇智信息技术有限公司 开发    百度统计

    x 关闭 永久关闭

    【温馨提醒】近日，《协和医学杂志》编辑部接到作者反映，有多名不法人员冒充期刊编辑发送见刊通知，鼓动作者添加微信，从而骗取版面费的行为。特提醒您，本刊与作者联系的方式均为邮件通知或电话，稿件进度通知邮箱为：mjpumch@126.com，编辑部电话为：010-69154261，请提高警惕，谨防上当受骗！如有任何疑问，请致电编辑部核实。谢谢！