Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.
Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.
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快速细菌全基因组测序，以增强诊断和公共卫生微生物学。
DOI：
10.1001/jamainternmed.2013.7734
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发表时间：
2013-08-12
影响因子：
39
通讯作者：
Peacock, Sharon J.
中科院分区：
文献类型：
--
作者：
Reuter, Sandra;Ellington, Matthew J.;Cartwright, Edward J. P.;Koeser, Claudio U.;Toeroek, M. Estee;Gouliouris, Theodore;Harris, Simon R.;Brown, Nicholas M.;Holden, Matthew T. G.;Quail, Mike;Parkhill, Julian;Smith, Geoffrey P.;Bentley, Stephen D.;Peacock, Sharon J.
最新一代台式DNA测序平台可以在不到一天的时间内为各种细菌提供准确的全基因组序列（WGS）。这些可以用来更有效地遏制耐多药病原体的传播。将WGS与标准临床微生物学实践进行比较，以调查由多重耐药菌引起的医院暴发，鉴定抗菌药物耐药性的遗传决定因素，以及对其他临床重要病原体进行分型。一项针对剑桥大学医院NHS基金会信托（英格兰二级和三级转诊中心）的一系列细菌感染住院患者的实验室研究，使用储存的细菌分离株和临床信息将WGS与标准诊断微生物学进行比较。作为常规临床护理的一部分，采集并处理标本，并储存培养分离株，并在必要时进行额外的参考实验室检测。分离株在Illumina MiSeq平台上测序之前进行DNA提取和文库制备。由对临床、流行病学和抗菌药物敏感性数据不知情的人员进行生物信息学分析。我们调查了2个假定的医院内暴发，一个由万古霉素耐药屎肠球菌引起，另一个由碳青霉烯耐药阴沟肠杆菌引起; WGS准确区分暴发和非暴发分离株，并且上级优于传统分型方法。我们比较了WGS与标准方法在一系列革兰氏阴性菌（鲍曼不动杆菌、大肠埃希菌、大肠埃希菌和肺炎克雷伯菌）中鉴定碳青霉烯耐药机制的结果。这证明了表型和基因型结果之间的一致性，以及确定耐药性是否归因于碳青霉烯酶或其他耐药机制的能力。全基因组测序用于概括脑膜炎奈瑟菌临床分离株的参考实验室分型，并提供这些菌株的扩展系统发育分析。WGS平台提供的信息的速度，准确性和深度，以确认或反驳医院和社区的疫情，并准确定义多重耐药和其他生物体的传播，代表了一个重要的进步。
The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.
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影响因子：
2.8
作者：
Hall, Barry G.;Ehrlich, Garth D.;Hu, Fen Z.
通讯作者：
Hu, Fen Z.
影响因子：
9.4
作者：
Nolte, Frederick S.;McAdam, Alexander J.
通讯作者：
McAdam, Alexander J.
影响因子：
6.4
作者：
Mathers AJ;Cox HL;Kitchel B;Bonatti H;Brassinga AK;Carroll J;Scheld WM;Hazen KC;Sifri CD
通讯作者：
Sifri CD
影响因子：
4.2
作者：
Qin X;Galloway-Peña JR;Sillanpaa J;Roh JH;Nallapareddy SR;Chowdhury S;Bourgogne A;Choudhury T;Muzny DM;Buhay CJ;Ding Y;Dugan-Rocha S;Liu W;Kovar C;Sodergren E;Highlander S;Petrosino JF;Worley KC;Gibbs RA;Weinstock GM;Murray BE
通讯作者：
Murray BE
影响因子：
12.3
作者：
Adey A;Morrison HG;Asan;Xun X;Kitzman JO;Turner EH;Stackhouse B;MacKenzie AP;Caruccio NC;Zhang X;Shendure J
通讯作者：
Shendure J