Bachmann Nathan L, Rockett Rebecca J, Timms Verlaine Joy, Sintchenko Vitali
Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.
Centenary Institute, University of Sydney, Camperdown, NSW, Australia.
Front Public Health. 2018 Dec 12;6:363. doi: 10.3389/fpubh.2018.00363. eCollection 2018.
Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.
全基因组测序（WGS）通过高分辨率的疫情追踪、实验室监测和诊断，在传染病控制中发挥着越来越重要的作用。然而，传统上全基因组测序依赖于微生物培养，以获取用于测序的病原体特异性DNA。这严重限制了全基因组测序在培养要求苛刻的病原体上的应用。此外，非培养诊断测试的广泛采用减少了用于确证测试和监测的培养分离株的可得性。这些最新进展催生了对实施无需培养分离株就能直接对临床样本中的微生物基因组进行测序的技术的需求。然而，临床样本中特定生物体的测序可能会受到来自宿主和其他共生微生物的高水平污染DNA的影响。已经引入了几种方法来选择性裂解宿主细胞和/或从临床样本中分离特定生物体。本综述探讨了诊断和公共卫生实验室用于宏基因组测序的不同样本制备方法。
