Satta, G;
Atzeni, A;
McHugh, TD;
(2017)
Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist.
Clinical Microbiology and Infection
, 23
(2)
pp. 69-72.
10.1016/j.cmi.2016.09.005.
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Abstract
Whole genome sequencing (WGS) has the potential to revolutionize the diagnosis of Mycobacterium tuberculosis (MTB) but the lack of bioinformatic expertise among clinical microbiologists is a barrier for adoption. Software products for analysis should be simple, free of charge, able to accept data directly from the sequencer (FASTQ files) and to provide the basic functionalities all-in-one. The main aim of this narrative review is to provide a practical guide for the clinical microbiologist, with little or no practical experience of WGS analysis, with a specific focus on software products tailored made for MTB analysis. With sequencing performed by an external provider, it is now feasible to implement WGS analysis in the routine clinical practice of any microbiology laboratory, with the potential to detect resistance weeks before traditional phenotypic culture methods, but the clinical microbiologist should be aware of the limitations of this approach.
| Type: | Article |
|---|---|
| Title: | Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.cmi.2016.09.005 |
| Publisher version: | http://dx.doi.org/10.1016/j.cmi.2016.09.005 |
| Language: | English |
| Additional information: | Copyright © 2016. This manuscript version is published under a Creative Commons Attribution Non-commercial Non-derivative 4.0 International licence (CC BY-NC-ND 4.0). This licence allows you to share, copy, distribute and transmit the work for personal and non-commercial use providing author and publisher attribution is clearly stated. Further details about CC BY licences are available at http://creativecommons.org/licenses/by/4.0. Access may be initially restricted by the publisher. |
| Keywords: | Mycobacterium tuberculosis; Phylogenetic analysis; Online tools; Rapid susceptibility testing; Whole genome sequencing, Analysis |
| 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 Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1517199 |
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