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.
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。
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This work was supported by the Medicine and Health, Science and Technology Plan Project of Zhejiang (Nos. 2020KY1009 and 2021KY387) and the Jinhua Science and Technology Planning Project Social Development Key Project (No. 2021-3-072), China.
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Ying LIU wrote the manuscript. Yongjun MA had the idea, revised the manuscript, and applied the project. Both authors have read and approved the final manuscript, and therefore, agreed to be responsible for the research integrity and for all aspects of the work.
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Liu, Y., Ma, Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J. Zhejiang Univ. Sci. B (2024). https://doi.org/10.1631/jzus.B2300029
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DOI: https://doi.org/10.1631/jzus.B2300029
Key words
- Metagenomics next-generation sequencing (mNGS)
- Infectious disease
- Cerebrospinal fluid (CSF)
- Oxford Nanopore Technologies (ONT)
- Microbiome