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    Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda

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    Meehan_Infection_Genetics_and_Evolution.pdf (848.0Kb)
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    Publication date
    2016-06
    Author
    Ssengooba, W.
    Meehan, Conor J.
    Lukoye, D.
    Kasule, G.W.
    Musisi, K.
    Joloba, M.L.
    Cobelens, F.G.
    de Jong, B.C.
    Keyword
    Whole genome sequencing
    Complement
    Tuberculosis
    Drug resistance surveys
    Rights
    © 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
    Peer-Reviewed
    Yes
    
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    Abstract
    Understanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.
    URI
    http://hdl.handle.net/10454/17316
    Version
    Published version
    Citation
    Ssengooba W, Meehan CJ, Lukoye D et al (2016) Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda. Infection, Genetics and Evolution. 40: 8-16.
    Link to publisher’s version
    https://doi.org/10.1016/j.meegid.2016.02.019
    Type
    Article
    Collections
    Life Sciences Publications

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