Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
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DOI：
10.1007/s10096-017-3024-6
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发表时间：
2017-11
期刊：
影响因子：
--
通讯作者：
Greub G
中科院分区：
文献类型：
--
作者：
Tagini F;Greub G
近年来，全基因组测序（WGS）被认为是一种有可能彻底改变临床微生物学的技术。在此，我们回顾了WGS用于临床微生物实验室中最常见病原体的文献：大肠杆菌和其他肠杆菌科，金黄色葡萄球菌和凝固酶阴性葡萄球菌，链球菌和肠球菌，分枝杆菌和沙眼衣原体。对于每个病原体组，我们重点关注五个不同的方面：基因组特征，最常见的基因组方法和WGS的临床用途（i）分型和爆发分析，（ii）毒力调查和（iii）计算机抗菌药物敏感性测试。在所有临床用途中，最常见和最直接的用途是对细菌进行分类并追溯爆发。由于基于WGS数据开发了几种新的全基因组多位点序列分型系统，标准化迈出了下一步。虽然毒力特性可以帮助在各种特定的临床环境中，它主要是用来描述爆发菌株。越来越多的研究比较了基因型和表型抗生素敏感性测试，大多数结果都很有希望。然而，常规实施将优先在特定病原体（如分枝杆菌）的工作流程中进行，而不是作为广泛适用的通用工具。总体而言，WGS在常规临床微生物学或感染控制实验室中的具体应用已经完成，但下一个重大挑战将是程序和生物信息学管道的标准化和验证，以达到临床标准。
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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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
链球菌基因组演化的机理。
影响因子：
3.2
作者：
Andam, Cheryl P.;Hanage, William P.
通讯作者：
Hanage, William P.
影响因子：
9.4
作者：
Bartels, Mette Damkjaer;Petersen, Andreas;Westh, Henrik
通讯作者：
Westh, Henrik
影响因子：
14.2
作者：
Andersson, P.;Klein, M.;Giffard, P. M.
通讯作者：
Giffard, P. M.
影响因子：
5.2
作者：
Chen, Chih-Jung;Huang, Yhu-Chering;Chiu, Cheng-Hsu
通讯作者：
Chiu, Cheng-Hsu