Deurenberg Ruud H, Bathoorn Erik, Chlebowicz Monika A, Couto Natacha, Ferdous Mithila, García-Cobos Silvia, Kooistra-Smid Anna M D, Raangs Erwin C, Rosema Sigrid, Veloo Alida C M, Zhou Kai, Friedrich Alexander W, Rossen John W A
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands; Certe, Department of Medical Microbiology, Groningen, The Netherlands.
J Biotechnol. 2017 Feb 10;243:16-24. doi: 10.1016/j.jbiotec.2016.12.022. Epub 2016 Dec 29.
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements.
当前人类病原体的分子诊断提供的信息有限,往往不足以进行疫情爆发和传播调查。下一代测序(NGS)可在一次测序运行中确定完整细菌基因组的DNA序列,并从这些数据中获得有关耐药性和毒力的信息以及分型信息,这对疫情调查很有用。所获得的基因组数据可进一步用于开发针对疫情的筛查检测方法。在本综述中,对NGS进行了一般性介绍,包括文库制备以及最常见的NGS平台(如MiSeq(Illumina)和Ion PGM™(赛默飞世尔))的主要特点。概述了荷兰格罗宁根大学医学中心医学微生物诊断实验室用于NGS数据分析的软件。此外,还描述了NGS在临床环境中的应用,如疫情管理、分子病例发现、病原体的特征分析和监测、利用16S - 23S rRNA区域快速鉴定细菌、分类学、对临床样本的宏基因组学方法以及人畜共患病微生物从动物到人的传播测定。最后,我们分享了对在不久的将来NGS在个性化微生物学中应用的展望,并指出了具体要求。