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

Balloux, F; Brønstad Brynildsrud, O; van Dorp, L; Shaw, LP; Chen, H; Harris, KA; Wang, H; (2018) From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends in Microbiology , 26 (12) pp. 1035-1048. 10.1016/j.tim.2018.08.004. Green open access

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Abstract

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.

Type: Article
Title: From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.tim.2018.08.004
Publisher version: http://doi.org/10.1016/j.tim.2018.08.004
Language: English
Additional information: Copyright © 2018 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Accessory genome, Antimicrobial resistance (AMR), Horizontal gene tranfer (HGT), K-mer, Multilocus sequence typing (MLST), Phylogenetic tree, Transmission chain, Virulence, Whole-genome sequencing (WGS)
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10056758
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