Li Na, Cai Qingqing, Miao Qing, Song Zeshi, Fang Yuan, Hu Bijie
Department of Infectious Diseases Zhongshan Hospital Fudan University Shanghai 200032 China.
Genoxor Medical Science and Technology Inc. Zhejiang 317317 China.
Small Methods. 2021 Jan 4;5(1):2000792. doi: 10.1002/smtd.202000792. Epub 2020 Dec 13.
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
由于技术的快速发展和成本的大幅降低，测序技术的应用正在从研究实验室转向临床实验室。然而，尽管已知有成千上万种微生物会感染人类，但由于目前的诊断方法只能识别一小部分病原体，因此确定许多疾病的病原体仍然具有挑战性。新病原体的出现使这些挑战更加复杂。因此，宏基因组下一代测序（mNGS）作为一种用于检测和分类表征微生物的无偏见、全面的方法，已成为一种有吸引力的策略。尽管许多研究和病例报告证实了mNGS在改善传染病的诊断、治疗和追踪方面的成功，但仍有几个障碍需要克服。因此，从业者和临床医生在将mNGS应用于临床实践时，必须了解其优点和局限性。有趣的是，新兴的第三代测序技术可能会部分抵消mNGS的缺点。在这篇综述中，主要描述了：a）测序技术的历史；b）各种NGS技术、常见平台以及临床应用的工作流程；c）NGS在病原体鉴定中的应用；d）全球专家对临床应用中NGS相关方法的共识；以及e）与诊断宏基因组学相关的挑战。
