Clinical detection and characterization of bacterial pathogens in the genomics era.
Clinical detection and characterization of bacterial pathogens in the genomics era.
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DOI：
10.1186/s13073-014-0114-2
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发表时间：
2014
期刊：
影响因子：
12.3
通讯作者：
Raoult D
中科院分区：
文献类型：
--
作者：
Fournier PE;Dubourg G;Raoult D
使用下一代测序(NGS)获得的基因组序列的可用性使传染病领域发生了革命性的变化。事实上，迄今已对38000多个细菌和5000多个病毒基因组进行了测序，其中包括所有重要的人类病原体的代表。这些海量的数据不仅使基础生物学的进步成为可能，有助于了解微生物的发病机制及其基因组进化，而且还对临床微生物学产生了影响。在这里，我们首先回顾基因组学在改进诊断工具方面的当前成就，包括那些现已在临床上可用的工具，例如用于检测微生物病原体、毒力因子或抗生素耐药决定因素的聚合酶链式反应分析的设计，或针对不可培养的病原体的优化培养基设计。然后，我们回顾了基因组学在暴发调查中的应用，无论是通过基因分型分析的设计还是对致病菌株的直接测序。最后，我们讨论了基因组学可能如何改变未来的临床微生物学。本文的在线版本(doi：10.1186/s13073-014-0114-2)包含补充材料，授权用户可以使用。
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for ‘unculturable’ pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future. The online version of this article (doi:10.1186/s13073-014-0114-2) contains supplementary material, which is available to authorized users.
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影响因子：
4.9
作者：
Buriánková, K;Doucet-Populaire, F;Pernodet, JL
通讯作者：
Pernodet, JL
DOI：
10.1073/pnas.0408026101
发表时间：
2004-12-21
影响因子：
11.1
作者：
Achtman, M;Morelli, G;Keim, P
通讯作者：
Keim, P
DOI：
10.1038/nrg3182
发表时间：
2012-03-13
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.7
作者：
Dugan VG;Emrich SJ;Giraldo-Calderón GI;Harb OS;Newman RM;Pickett BE;Schriml LM;Stockwell TB;Stoeckert CJ Jr;Sullivan DE;Singh I;Ward DV;Yao A;Zheng J;Barrett T;Birren B;Brinkac L;Bruno VM;Caler E;Chapman S;Collins FH;Cuomo CA;Di Francesco V;Durkin S;Eppinger M;Feldgarden M;Fraser C;Fricke WF;Giovanni M;Henn MR;Hine E;Hotopp JD;Karsch-Mizrachi I;Kissinger JC;Lee EM;Mathur P;Mongodin EF;Murphy CI;Myers G;Neafsey DE;Nelson KE;Nierman WC;Puzak J;Rasko D;Roos DS;Sadzewicz L;Silva JC;Sobral B;Squires RB;Stevens RL;Tallon L;Tettelin H;Wentworth D;White O;Will R;Wortman J;Zhang Y;Scheuermann RH
通讯作者：
Scheuermann RH
影响因子：
11.8
作者：
Drancourt M;Roux V;Dang LV;Tran-Hung L;Castex D;Chenal-Francisque V;Ogata H;Fournier PE;Crubézy E;Raoult D
通讯作者：
Raoult D