Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.

中文翻译：

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临床元基因组下一代测序用于病原体检测。

几乎所有的传染原都包含DNA或RNA基因组，这使得测序成为一种有吸引力的病原体检测方法。自2004年问世以来，高通量测序或下一代测序的成本已降低了几个数量级，它已成为检测和鉴定患者临床样品中微生物的有效技术平台。这篇综述着重于未靶向的宏基因组下一代测序技术在传染病临床诊断中的应用，特别是在传统诊断方法存在局限性的领域。该审查涵盖（a）下一代测序技术和通用平台，（b）临床微生物学实验室中的下一代测序测定工作流程，（c）宏基因组新一代测序数据的生物信息学分析，（d）宏基因组新一代测序在传染病诊断中的验证和使用，以及（e）该领域的重要病例报告和研究。下一代测序是一项新技术，有望增强我们诊断，询问和跟踪传染病的能力。