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.

中文翻译：

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用于临床环境中病原体鉴定的高通量宏基因组学

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转向临床实验室。然而，尽管已知有数千种微生物可感染人类，但许多疾病的病原体鉴定仍然具有挑战性，因为目前的诊断方法只能鉴定一小部分病原体。新病原体的出现加剧了这些挑战。因此，宏基因组下一代测序（mNGS）作为一种不可知的、公正的、全面的微生物检测和分类学表征方法，已成为一种有吸引力的策略。尽管许多研究和病例报告已证实 mNGS 在改善传染病的诊断、治疗和追踪方面取得了成功，但仍需克服一些障碍。因此，从业者和临床医生在将其应用于临床实践时必须了解 mNGS 的优点和局限性。有趣的是，新兴的第三代测序技术可能部分抵消mNGS的缺点。本次回顾主要是：a）测序技术的历史；b) 临床应用的各种NGS技术、通用平台和工作流程；c) NGS在病原体鉴定中的应用；d) NGS相关方法临床应用的全球专家共识；e) 描述了与诊断宏基因组学相关的挑战。