From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
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DOI：
10.1016/j.tim.2018.08.004
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发表时间：
2018-12
影响因子：
15.9
通讯作者：
Eldholm V
中科院分区：
文献类型：
--
作者：
Balloux F;Brønstad Brynildsrud O;van Dorp L;Shaw LP;Chen H;Harris KA;Wang H;Eldholm V
世界各地的医院都面临着越来越多的难以治疗的感染。限制感染并为患者提供最佳药物方案需要及时进行菌株鉴定以及毒力和耐药性分析。此外，预防性干预基于对复发性感染的环境来源的识别（例如，污染的汇）和传播链的重建（即，谁感染了谁）可以帮助降低医院感染的发生率。WGS可能是解决这些问题的关键。然而，在临床上的应用一直很缓慢。在WGS发挥其在临床微生物诊断方面的潜力之前，需要解决一些重大的科学和后勤挑战。在这篇综述中，我们确定了WGS需要解决的主要瓶颈，以定期通知临床干预，并讨论可能的解决方案。原则上，WGS可以近实时地为临床微生物学提供高度相关的信息，从表型检测到跟踪疫情。然而，尽管有这样的前景，但迄今为止，WGS在临床上的应用仍然有限，未来的实施可能是一个缓慢的过程。WGS提供的越来越多的信息可能会与传统的微生物概念和分型方案产生冲突。降低原始测序成本并没有转化为降低细菌基因组的总成本，细菌基因组已经稳定。现有的研究管道不适合临床，应开发定制的临床管道。
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions. In principle, WGS can provide highly relevant information for clinical microbiology in near-real-time, from phenotype testing to tracking outbreaks. However, despite this promise, the uptake of WGS in the clinic has been limited to date, and future implementation is likely to be a slow process. The increasing information provided by WGS can cause conflict with traditional microbiological concepts and typing schemes. Decreasing raw sequencing costs have not translated into decreasing total costs for bacterial genomes, which have stabilised. Existing research pipelines are not suitable for the clinic, and bespoke clinical pipelines should be developed.
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影响因子：
10.7
作者：
Depledge DP;Kundu S;Jensen NJ;Gray ER;Jones M;Steinberg S;Gershon A;Kinchington PR;Schmid DS;Balloux F;Nichols RA;Breuer J
通讯作者：
Breuer J
影响因子：
6.4
作者：
Didelot X;Dordel J;Whittles LK;Collins C;Bilek N;Bishop CJ;White PJ;Aanensen DM;Parkhill J;Bentley SD;Spratt BG;Harris SR
通讯作者：
Harris SR
影响因子：
16.6
作者：
Bradley P;Gordon NC;Walker TM;Dunn L;Heys S;Huang B;Earle S;Pankhurst LJ;Anson L;de Cesare M;Piazza P;Votintseva AA;Golubchik T;Wilson DJ;Wyllie DH;Diel R;Niemann S;Feuerriegel S;Kohl TA;Ismail N;Omar SV;Smith EG;Buck D;McVean G;Walker AS;Peto TE;Crook DW;Iqbal Z
通讯作者：
Iqbal Z
DOI：
10.1073/pnas.1611283113
发表时间：
2016-11-29
影响因子：
11.1
作者：
Eldholm, Vegard;Pettersson, John H. -O.;Balloux, Francois
通讯作者：
Balloux, Francois
影响因子：
3.9
作者：
Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
通讯作者：
Aanensen DM