Lefterova Martina I, Suarez Carlos J, Banaei Niaz, Pinsky Benjamin A
Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California.
Association for Molecular Pathology Next-Generation Sequencing in Infectious Disease Work Group, Bethesda, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California.
J Mol Diagn. 2015 Nov;17(6):623-34. doi: 10.1016/j.jmoldx.2015.07.004. Epub 2015 Sep 30.
Next-generation sequencing (NGS) technologies are increasingly being used for diagnosis and monitoring of infectious diseases. Herein, we review the application of NGS in clinical microbiology, focusing on genotypic resistance testing, direct detection of unknown disease-associated pathogens in clinical specimens, investigation of microbial population diversity in the human host, and strain typing. We have organized the review into three main sections: i) applications in clinical virology, ii) applications in clinical bacteriology, mycobacteriology, and mycology, and iii) validation, quality control, and maintenance of proficiency. Although NGS holds enormous promise for clinical infectious disease testing, many challenges remain, including automation, standardizing technical protocols and bioinformatics pipelines, improving reference databases, establishing proficiency testing and quality control measures, and reducing cost and turnaround time, all of which would be necessary for widespread adoption of NGS in clinical microbiology laboratories.
新一代测序（NGS）技术越来越多地用于传染病的诊断和监测。在此，我们综述了NGS在临床微生物学中的应用，重点关注基因型耐药性检测、临床标本中未知疾病相关病原体的直接检测、人类宿主中微生物种群多样性的研究以及菌株分型。我们将综述分为三个主要部分：i）在临床病毒学中的应用，ii）在临床细菌学、分枝杆菌学和真菌学中的应用，以及iii）验证、质量控制和能力维持。尽管NGS在临床传染病检测方面前景广阔，但仍存在许多挑战，包括自动化、技术方案和生物信息学流程的标准化、改进参考数据库、建立能力验证和质量控制措施以及降低成本和周转时间，所有这些都是NGS在临床微生物学实验室广泛应用所必需的。
