Practical Issues in Implementing Whole-Genome-Sequencing in Routine Diagnostic Microbiology Genomic and Molecular Diagnostics
Practical Issues in Implementing Whole-Genome-Sequencing in Routine Diagnostic Microbiology Genomic and Molecular Diagnostics
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发表时间：
2018
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通讯作者：
Microbiology;Rossen;Moran-Gilad
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作者：
Microbiology;Rossen;Moran-Gilad
背景：下一代测序（NGS）在临床微生物学中的应用越来越广泛。就像微生物学中采用的每一项新技术一样，必须仔细管理将NGS整合到临床和日常工作流程中。目的：综述常规诊断实验室实施细菌全基因组测序（WGS）的实际情况。资料来源：文献综述和专家意见。内容：本文讨论了何时及如何将全基因组测序纳入临床实验室的日常工作流程。此外，由于微生物实验室必须遵守各种国家和国际法规和标准才能获得认可，我们讨论了在微生物学中使用WGS的质量控制问题，包括专业测试的重要性。此外，还描述了该技术在微生物学诊断层次中的当前和未来地位，以及与已建立的方法保持向后兼容性的必要性。最后，我们推测WGS是否可以在未来完全取代常规微生物学的问题，以及大多数测序仪设计用于并行处理多个样品，而优选逐个处理样品以获得最佳诊断这一事实之间的紧张关系。特别提到了诊断实验室WGS的成本和周转时间。影响：需要进一步开发以改善WGS的工作流程，特别是缩短周转时间、降低成本和简化下游数据分析。只有当这些过程成熟时，依赖WGS进行常规患者管理和感染控制管理才变得可行，从而使临床微生物学转变为基于基因组和个性化的诊断领域。J.W.A. Rossen，临床微生物感染2018；24:355©2017作者。由爱思唯尔有限公司代表欧洲临床微生物学和传染病学会出版。这是一篇基于CC BY-NC-ND许可（http:// creativecommons.org/licenses/by-nc-nd/4.0/）的开放获取文章。
Background: Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine work-fl ows must be carefully managed. Aim: To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. Sources: Review of the literature and expert opinion. Content: In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine work fl ow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of pro fi ciency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbi- ology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. Implications: Further development is required to improve the work fl ow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic fi eld. J.W.A. Rossen, Clin Microbiol Infect 2018;24:355 © 2017 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).