Clinical applications of metagenomics next-generation sequencing in infectious diseases

Ying LIU; Yongjun MA

doi:10.1631/jzus.B2300029

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Review | Updated：2024-06-24

Clinical applications of metagenomics next-generation sequencing in infectious diseases
Clinical applications of metagenomics next-generation sequencing in infectious diseases
宏基因组二代测序技术（mNGS）在感染性疾病中的临床应用
Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology) Vol. 25, Issue 6, Pages: 471-484(2024)
Affiliations：

Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
Funds：
DOI：10.1631/jzus.B2300029
CLC：
CSTR：
Published： 15 June 2024 ，

Published Online： 17 May 2024 ，

Received： 09 January 2023 ，

Revised： 06 June 2023 ，

刘颖,马拥军.宏基因组二代测序技术（mNGS）在感染性疾病中的临床应用[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2024,25(06):471-484.

Ying LIU, Yongjun MA. Clinical applications of metagenomics next-generation sequencing in infectious diseases. [J]. Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology) 25(6):471-484(2024)
刘颖,马拥军.宏基因组二代测序技术（mNGS）在感染性疾病中的临床应用[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2024,25(06):471-484. DOI： 10.1631/jzus.B2300029.

Ying LIU, Yongjun MA. Clinical applications of metagenomics next-generation sequencing in infectious diseases. [J]. Journal of Zhejiang University-SCIENCE B (Biomedicine & Biotechnology) 25(6):471-484(2024) DOI： 10.1631/jzus.B2300029.

摘要

传染病对人类健康产生巨大威胁。快速准确地检测出病原体对于传染病的诊断和治疗非常重要。宏基因组二代测序技术（mNGS）能无差别检测样本中所有的核酸（DNA和RNA）。随着测序和生物信息学技术的发展，mNGS正从实验室研究向临床应用迈进，为病原体检测开辟了新的途径。大量研究表明，mNGS在感染性疾病的临床应用中具有良好的潜力，尤其适用于难检测、罕见和新型病原。但是，mNGS在临床应用中仍存在一些问题:（1）缺乏通用的、可验证的工作流程和质量保证；（2）对高宿主背景和低生物量的样本不敏感；（3）缺乏对海量数据分析和报告解读的标准化指导。因此，全面了解这项新技术将有助于促进mNGS在感染性疾病中的临床应用。本文简要综述了二代测序技术的发展历史、主流测序平台和mNGS工作流程，并讨论了mNGS在感染性疾病中的临床应用及该技术的优缺点。

Abstract

Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies

mNGS is moving from research to clinical application

which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases

especially in difficult-to-detect

rare

and novel pathogens. However

there are several hurdles in the clinical application of mNGS

such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore

a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing

mainstream sequencing platforms

and mNGS workflow

and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.

关键词

宏基因组二代测序技术（mNGS）感染性疾病脑脊液（CSF）牛津纳米孔技术（ONT）微生物群

Keywords

Metagenomics next-generation sequencing (mNGS)Infectious diseaseCerebrospinal fluid (CSF)Oxford Nanopore Technologies (ONT)Microbiome

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