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Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum

Nimmo, C; Doyle, R; Burgess, C; Williams, R; Gorton, R; McHugh, TD; Brown, M; ... Breuer, J; + view all (2017) Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum. International Journal of Infectious Diseases , 62 pp. 44-46. 10.1016/j.ijid.2017.07.007. Green open access

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Abstract

INTRODUCTION: Resistance to second line tuberculosis drugs is common, but slow to diagnose with phenotypic drug sensitivity testing. Rapid molecular tests speed up diagnosis, but can only detect limited mutations. Whole genome sequencing (WGS) of culture isolates can generate a complete genetic drug resistance profile, but is delayed by the initial culture step. We previously successfully achieved WGS directly from sputum using targeted enrichment. CASE REPORT: A 29-year-old Nigerian lady was diagnosed with tuberculosis. Xpert MTB/RIF and Hain line probe assays identified rpoB and inhA mutations consistent with rifampicin and intermediate isoniazid resistance, and a further possible mutation conferring fluoroquinolone resistance. WGS directly from sputum identified a further inhA mutation consistent with high level isoniazid resistance and confirmed absence of fluoroquinolone resistance. Isoniazid was stopped and she has completed 18 months of a fluoroquinolone-based regimen without relapse. DISCUSSION: Compared to rapid molecular tests which can only examine a limited number of mutations, and WGS of culture isolates which requires a culture step, WGS directly from sputum can quickly generate a complete genetic drug resistance profile. In this case WGS altered clinical management of drug-resistant tuberculosis, and demonstrates potential to guide individualised drug treatment where second line drug resistance is common.

Type: Article
Title: Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ijid.2017.07.007
Publisher version: http://dx.doi.org/10.1016/j.ijid.2017.07.007
Language: English
Additional information: This is an article under a Creative Commons license Attribution 4.0 International (CC BY 4.0)
Keywords: Tuberculosis; whole genome sequencing; drug resistance; clinical samples; directly from sputum
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
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
URI: https://discovery.ucl.ac.uk/id/eprint/1565301
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