From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

被引：117

作者：

Balloux, Francois ^{[1
]}

Brynildsrud, Ola Bronstad ^{[2
]}

van Dorp, Lucy ^{[1
]}

Shaw, Liam P. ^{[1
]}

Chen, Hongbin ^{[1
,3
]}

Harris, Kathryn A. ^{[4
]}

Wang, Hui ^{[3
]}

Eldholm, Vegard ^{[2
]}

机构：

[1] UCL, UCL Genet Inst, Gower St, London WC1E 6BT, England

[2] Norwegian Inst Publ Hlth, Infect Dis & Environm Hlth, Lovisenberggata 8, N-0456 Oslo, Norway

[3] Peking Univ, Dept Clin Lab, Peoples Hosp, Beijing 100044, Peoples R China

[4] Great Ormond St Hosp NHS Fdn Trust, Dept Microbiol Virol & Infect Prevent & Control, London WC1N 3JH, England

来源：

TRENDS IN MICROBIOLOGY | 2018年 / 26卷 / 12期

基金：

中国国家自然科学基金; 英国生物技术与生命科学研究理事会;

关键词：

STAPHYLOCOCCUS-AUREUS; ANTIBIOTIC-RESISTANCE; REAL-TIME; ANTIMICROBIAL RESISTANCE; EVOLUTION; TRANSMISSION; TUBERCULOSIS; VIRUS; SURVEILLANCE; PATHOGEN;

D O I：

10.1016/j.tim.2018.08.004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1035 / 1048

页数：14

共 83 条

[1] Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica [J].

Achtman, Mark ;

Wain, John ;

Weill, Francois-Xavier ;

Nair, Satheesh ;

Zhou, Zhemin ;

Sangal, Vartul ;

Krauland, Mary G. ;

Hale, James L. ;

Harbottle, Heather ;

Uesbeck, Alexandra ;

Dougan, Gordon ;

Harrison, Lee H. ;

Brisse, Sylvain .

PLOS PATHOGENS, 2012, 8 (06)

[2] Microreact: visualizing and sharing data for genomic epidemiology and phylogeography [J].

Argimon, Silvia ;

Abudahab, Khalil ;

Goater, Richard J. E. ;

Fedosejev, Artemij ;

Bhai, Jyothish ;

Glasner, Corinna ;

Feil, Edward J. ;

Holden, Matthew T. G. ;

Yeats, Corin A. ;

Grundmann, Hajo ;

Spratt, Brian G. ;

Aanensen, David M. .

MICROBIAL GENOMICS, 2016, 2 (11) :e000093

[3] Spatiotemporal microbial evolution on antibiotic landscapes [J].

Baym, Michael ;

Lieberman, Tami D. ;

Kelsic, Eric D. ;

Chait, Remy ;

Gross, Rotem ;

Yelin, Idan ;

Kishony, Roy .

SCIENCE, 2016, 353 (6304) :1147-1151

[4] Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori [J].

Björkholm, B ;

Sjölund, M ;

Falk, PG ;

Berg, OG ;

Engstrand, L ;

Andersson, DI .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (25) :14607-14612

[5] BEAST 2: A Software Platform for Bayesian Evolutionary Analysis [J].

Bouckaert, Remco ;

Heled, Joseph ;

Kuehnert, Denise ;

Vaughan, Tim ;

Wu, Chieh-Hsi ;

Xie, Dong ;

Suchard, Marc A. ;

Rambaut, Andrew ;

Drummond, Alexei J. .

PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (04)

[6] Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis [J].

Bradley, Phelim ;

Gordon, N. Claire ;

Walker, Timothy M. ;

Dunn, Laura ;

Heys, Simon ;

Huang, Bill ;

Earle, Sarah ;

Pankhurst, Louise J. ;

Anson, Luke ;

de Cesare, Mariateresa ;

Piazza, Paolo ;

Votintseva, Antonina A. ;

Golubchik, Tanya ;

Wilson, Daniel J. ;

Wyllie, David H. ;

Diel, Roland ;

Niemann, Stefan ;

Feuerriegel, Silke ;

Kohl, Thomas A. ;

Ismail, Nazir ;

Omar, Shaheed V. ;

Smith, E. Grace ;

Buck, David ;

McVean, Gil ;

Walker, A. Sarah ;

Peto, Tim E. A. ;

Crook, Derrick W. ;

Iqbal, Zamin .

NATURE COMMUNICATIONS, 2015, 6

[7]

Brandt C., 2017, SCI REP, V7, P13

[8] Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis [J].

Briese, Thomas ;

Kapoor, Amit ;

Mishra, Nischay ;

Jain, Komal ;

Kumar, Arvind ;

Jabado, Omar J. ;

Lipkin, W. Ian .

MBIO, 2015, 6 (05)

[9] Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples [J].

Brown, Amanda C. ;

Bryant, Josephine M. ;

Einer-Jensen, Katja ;

Holdstock, Jolyon ;

Houniet, Darren T. ;

Chan, Jacqueline Z. M. ;

Depledge, Daniel P. ;

Nikolayevskyy, Vladyslav ;

Broda, Agnieszka ;

Stone, Madeline J. ;

Christiansen, Mette T. ;

Williams, Rachel ;

McAndrew, Michael B. ;

Tutill, Helena ;

Brown, Julianne ;

Melzer, Mark ;

Rosmarin, Caryn ;

McHugh, Timothy D. ;

Shorten, Robert J. ;

Drobniewski, Francis ;

Speight, Graham ;

Breuer, Judith .

JOURNAL OF CLINICAL MICROBIOLOGY, 2015, 53 (07) :2230-2237

[10] Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients [J].

Brown, Julianne R. ;

Morfopoulou, Sofia ;

Hubb, Jonathan ;

Emmett, Warren A. ;

Ip, Winnie ;

Shah, Divya ;

Brooks, Tony ;

Paine, Simon M. L. ;

Anderson, Glenn ;

Virasami, Alex ;

Tong, C. Y. William ;

Clark, Duncan A. ;

Plagnol, Vincent ;

Jacques, Thomas S. ;

Qasim, Waseem ;

Hubank, Mike ;

Breuer, Judith .

CLINICAL INFECTIOUS DISEASES, 2015, 60 (06) :881-888

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