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2025年·卷4·期  1 / 2
2024年·卷3·期  1
2023年·卷2·期  1
2022年·卷1·期  1

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基于宏基因组测序的临床病原体检测技术研究进展及临床应用

Metagenomic Next-Generation Sequencing in Clinical Pathogen Detection: Applications, Challenges, and Future Directions

作者：吴婉清1, 3, 5 ，喻鑫杰1, 3, 5，王苗苗2，谢沈博6，刘学英2，赵鹏飞4，杨励勤5，郑艺5，蔡霈5，潘文京1，刘洪娜1, *
1南华大学 未来科学研究院 衡阳医学院 湖南 衡阳
2湖南工业大学 医用纳米材料与器件湖南省重点实验室 湖南 株洲
3南华大学附属第一医院 检验科 湖南 衡阳
4安徽中医药大学 安徽 合肥
5南华大学 湖南省妇幼保健院 湖南 长沙
6 伦敦大学学院 人口与健康学院 儿童健康部门 细胞与基因治疗专业 英国 伦敦
*通信作者：刘洪娜；单位：南华大学 未来科学研究院 衡阳医学院 湖南 衡阳
环球医学进展, 2025, 4(2), 22-30;
提交日期 : 2025年09月02日 丨 录用日期 : 2025年10月09日 丨 出版日期 : 2025年10月31日
课题资助：四大慢病重大专项（编号：2023ZD0507400，2023ZD050740X），湖南省自然科学基金（编号：2023JJ50199，2025JJ80663），湖南省教育厅科学研究项目（编号：22A0385），2025年度湖南省重点研发计划（编号：2025JK2134），湖南省卫生健康委基金（编号：W20243057，D202302046032）
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摘 要：
宏基因组测序以其广谱、无偏、无需培养的特点，正改变临床感染诊断模式。其在未知或罕见病原体识别、混合感染解析、免疫抑制人群管理、脑炎等低丰度病原检测以及耐药基因预测方面均表现出显著优势。宏基因组测序还可以用于耐药性监测、传播链分析和公共卫生预警，扩展传统检测的能力。然而，其临床应用仍受宿主背景高、缺乏统一标准、定量能力有限、成本较高等因素限制。随着富集技术、测序技术、自动化流程及人工智能算法的发展，宏基因组测序有望实现更高灵敏度、更快周转时间和更规范的临床应用，为精准感染诊疗与公共卫生监测提供重要支撑。
关键词：宏基因组测序；病原体检测；感染性疾病；免疫抑制；自动化平台
 
Abstract:
Metagenomic next-generation sequencing (mNGS) has emerged as a powerful, unbiased diagnostic tool that overcomes the limitations of conventional culture and targeted assays. Its broad pathogen coverage enables rapid identification of rare, novel, and mixed infections, particularly benefiting critically ill and immunocompromised patients. mNGS also supports antimicrobial-resistance profiling, host–pathogen interaction analysis, and epidemiological surveillance. Despite these advantages, several challenges hinder routine clinical adoption, including high host-background interference, limited quantitative accuracy, and lack of standardized workflows across laboratories. Additionally, database errors, contamination control, and the balance between sequencing depth, sensitivity, and cost remain key constraints. Advances in host-depletion methods, long-read sequencing, automation, and AI-driven bioinformatics are expected to improve sensitivity, interpretability, and turnaround time. With expanding evidence from real-world studies, mNGS is poised to evolve from an innovative diagnostic approach into a comprehensive platform for pathogen detection, resistance assessment, and public-health monitoring.
Keywords: Metagenomic Next-generation Sequencing; Pathogen Detection; Infectious Diseases; Immunosuppression; Automated Platform
 
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参考文献 / References： 
  1. Schirmer M, Garner A, Vlamakis H, et al. Microbial Genes And Pathways Ininflammatory Bowel Disease. Nat Rev Microbiol. 2019 Aug;17(8):497-511. doi: 10.1038/s41579-019-0213-6.  
      
  2. Daniel R. The metagenomics of soil. Nat Rev Microbiol. 2005 Jun;3(6):470-8. doi: 10.1038/nrmicro1160.
  3. Jain S, Self WH, Wunderink RG, et al. Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults. The New England journal of medicine. 2015 Jul 30;373(5):415-27. doi: 10.1056/NEJMoa1500245.
  4. Babiker A, Bradley HL, Stittleburg VD, et al. Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19. J Clin Microbiol. 2020 Dec 17;59(1):e02142-20. doi: 10.1128/JCM.02142-20.
  5. 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 doi: 10.3389/fcimb.2018.0020510.3389/fcimb.2018.00205.s001.
  6. 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 Adv Res. 2021 Sep 29;38:201-212. doi: 10.1016/j.jare.2021.09.012.
  7. Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J. 2021;19:1497–1511. doi: 10.1016/j.csbj.2021.02.020. 
  8. Van Boheemen S, van Rijn AL, Pappas N, et al. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. J Mol Diagn. 2020;22(2):196–207. doi: 10.1016/j.jmoldx.2019.10.007.
  9. Simner PJ, Miller S, Carroll KC. Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases. Clin Infect Dis. 2018 Feb 10;66(5):778–788. doi: 10.1093/cid/cix881.
  10. Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol. 2019;37(7):783–792. doi: 10.1038/s41587-019-0156-5. 
  11. 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. Proceedings of the National Academy of Sciences of the United States of America. 2018 Dec 26;115(52):E12353-e12362. doi: 10.1073/pnas.1809700115.
  12. Miao Q, Ma Y, Wang Q, et al. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice. Clin Infect Dis. 2018 Nov 13;67(suppl_2):S231-S240. doi: 10.1093/cid/ciy693.
  13. Ding H, Huang J, Lin L, et al. Shedding light on negative cultures in osteoarticular infections: leveraging mNGS to unravel risk factors and microbial profiles. Front Cell Infect Microbiol. 2024 Nov 25;14:1457639. doi: 10.3389/fcimb.2024.1457639.
  14. Yang J, Yang F, Ren L, et al. Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol. 2011 Oct;49(10):3463-9. doi: 10.1128/JCM.00273-11.
  15. Chen HW, Fang ZS, Chen YT, et al. Targeting and Enrichment of Viral Pathogen by Cell Membrane Cloaked Magnetic Nanoparticles for Enhanced Detection. ACS Appl Mater Interfaces. 2017 Nov 22;9(46):39953-39961. doi: 10.1021/acsami.7b09931.
  16. Gu W, Crawford ED, O’Donovan BD, et al. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016;17(1) doi: 10.1186/s13059-016-0904-5. 
  17. Licheri M, Licheri MF, Probst L, et al. A novel isothermal whole genome sequencing approach for Monkeypox Virus. Sci Rep. 2024 Sep 27;14(1):22333. doi: 10.1038/s41598-024-73613-3. Erratum in: Sci Rep. 2025 Feb 5;15(1):4346. doi: 10.1038/s41598-025-88455-w.
  18. Zhang Y, Ai JW, Cui P, et al. A cluster of cases of pneumocystis pneumonia identified by shotgun metagenomics approach. J Infect. 2019 Feb;78(2):158-169. doi: 10.1016/j.jinf.2018.08.013.
  19. Gao D, Hu Y, Jiang X, et al. Applying the pathogen-targeted next-generation sequencing method to pathogen identification in cerebrospinal fluid. Ann Transl Med. 2021 Nov;9(22):1675. doi: 10.21037/atm-21-5488.
  20. Yee R, Breitwieser FP, Hao S, et al. Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms. Eur J Clin Microbiol Infect Dis. 2021 Jan;40(1):95-102. doi: 10.1007/s10096-020-03996-4.
  21. Zhu Na, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. The New England journal of medicine. 2020;382(8):727–733. doi: 10.1056/NEJMoa2001017. 
  22. Sun L, Zhang S, Yang Z, et al. Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis. Front Cell Infect Microbiol. 2022 Jul 13;12:905132. doi: 10.3389/fcimb.2022.905132.
  23. Wang J, Han Y, Feng J. Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis. BMC Pulmonary Medicine. 2019;19(1) doi: 10.1186/s12890-019-1022-4.
  24. Babiker A, Bradley HL, Stittleburg VD, et al. Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19. Journal of clinical microbiology. 2020 Oct 16. doi: 10.1128/JCM.02142-20. 
  25. Goldberg B, Sichtig H, Geyer C, et al. Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics. mBio. 2015 Dec 8;6(6):e01888-15. doi: 10.1128/mBio.01888-15.
  26. Xing XW, Zhang JT, Ma YB, et al. Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Encephalitis and Meningitis: A Large, Prospective Case Series of 213 Patients. Front Cell Infect Microbiol. 2020 Mar 5;10:88. doi: 10.3389/fcimb.2020.00088.
  27. Serpa PH, Deng X, Abdelghany M, et al. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. Genome Med. 2022 Jul 12;14(1):74. doi: 10.1186/s13073-022-01072-4.
  28. Harrison EM, Paterson GK, Holden MTG, et al. Whole Genome Sequencing Identifies Zoonotic Transmission Of Mrsa Isolates With The Novel Meca Homologue Mecc. EMBO Mol Med. 2013 Apr;5(4):509-15. doi: 10.1002/emmm.201202413.
  29. Sachsenröder J, Braun A, Machnowska P, et al. Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus. J Gen Virol. 2014 Dec;95(Pt 12):2734-2747. doi: 10.1099/vir.0.070029-0.
  30. Yang J, Li L, Zhu X, et al. Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS. Infect Drug Resist. 2023 Aug 8;16:5121-5134. doi: 10.2147/IDR.S421702.
  31. Jin X, Zhang Y, Zhang P, et al. The Structure And Function Of The Global Citrus Rhizosphere Microbiome.  Nat Commun. 2018 Nov 20;9(1):4894. doi: 10.1038/s41467-018-07343-2.
  32. Schlaberg R, Chiu CY, Miller S, et al. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Arch Pathol Lab Med. 2017;141(6):776–786. doi: 10.5858/arpa.2016-0539-RA.
  33. Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform. 2019 Jul 19;20(4):1125-1136. doi: 10.1093/bib/bbx120.
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