Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Francesc Coll; Ruth McNerney; Mark D. Preston; José Afonso Guerra-Assunção; Andrew Warry; Grant Hill-Cawthorne; Kim Mallard; Mridul Nair; Anabela Miranda; Adriana Alves; João Perdigão; Miguel Viveiros; Isabel Portugal; Zahra Hasan; Rumina Hasan; Judith R. Glynn; Nigel Martin; Arnab Pain; Taane G. Clark

doi:10.1186/s13073-015-0164-0

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Francesc Coll, Ruth McNerney, Mark D. Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant Hill-Cawthorne, Kim Mallard, Mridul Nair, Anabela Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R. Glynn, Nigel Martin, Arnab Pain, Taane G. Clark

Department of Pathology and Laboratory Medicine, Medical College, Pakistan

Research output: Contribution to journal › Article › peer-review

273 Citations (Scopus)

Abstract

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online 'TB-Profiler' tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.

Original language	English
Article number	51
Journal	Genome Medicine
Volume	7
Issue number	1
DOIs	https://doi.org/10.1186/s13073-015-0164-0
Publication status	Published - 14 Dec 2015

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10.1186/s13073-015-0164-0

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Coll, F., McNerney, R., Preston, M. D., Guerra-Assunção, J. A., Warry, A., Hill-Cawthorne, G., Mallard, K., Nair, M., Miranda, A., Alves, A., Perdigão, J., Viveiros, M., Portugal, I., Hasan, Z., Hasan, R., Glynn, J. R., Martin, N., Pain, A., & Clark, T. G. (2015). Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine, 7(1), Article 51. https://doi.org/10.1186/s13073-015-0164-0

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abstract = "Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online 'TB-Profiler' tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.",

author = "Francesc Coll and Ruth McNerney and Preston, {Mark D.} and Guerra-Assun{\c c}{\~a}o, {Jos{\'e} Afonso} and Andrew Warry and Grant Hill-Cawthorne and Kim Mallard and Mridul Nair and Anabela Miranda and Adriana Alves and Jo{\~a}o Perdig{\~a}o and Miguel Viveiros and Isabel Portugal and Zahra Hasan and Rumina Hasan and Glynn, {Judith R.} and Nigel Martin and Arnab Pain and Clark, {Taane G.}",

note = "Funding Information: This work was funded by the Bloomsbury Research Fund, Funda{\c c}{\~a}o para a Ci{\^e}ncia e Tecnologia, King Abdullah University of Science and Technology (KAUST), Medical Research Council UK (grant number MR/K000551/1) and the Wellcome Trust (grant number 096249/Z/11/B). Publisher Copyright: {\textcopyright} 2015 Coll et al. licensee BioMed Central.",

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Coll, F, McNerney, R, Preston, MD, Guerra-Assunção, JA, Warry, A, Hill-Cawthorne, G, Mallard, K, Nair, M, Miranda, A, Alves, A, Perdigão, J, Viveiros, M, Portugal, I, Hasan, Z , Hasan, R, Glynn, JR, Martin, N, Pain, A & Clark, TG 2015, 'Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences', Genome Medicine, vol. 7, no. 1, 51. https://doi.org/10.1186/s13073-015-0164-0

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AU - Coll, Francesc

AU - McNerney, Ruth

AU - Preston, Mark D.

AU - Guerra-Assunção, José Afonso

AU - Warry, Andrew

AU - Hill-Cawthorne, Grant

AU - Mallard, Kim

AU - Nair, Mridul

AU - Miranda, Anabela

AU - Alves, Adriana

AU - Perdigão, João

AU - Viveiros, Miguel

AU - Portugal, Isabel

AU - Hasan, Zahra

AU - Hasan, Rumina

AU - Glynn, Judith R.

AU - Martin, Nigel

AU - Pain, Arnab

AU - Clark, Taane G.

N1 - Funding Information: This work was funded by the Bloomsbury Research Fund, Fundação para a Ciência e Tecnologia, King Abdullah University of Science and Technology (KAUST), Medical Research Council UK (grant number MR/K000551/1) and the Wellcome Trust (grant number 096249/Z/11/B). Publisher Copyright: © 2015 Coll et al. licensee BioMed Central.

PY - 2015/12/14

Y1 - 2015/12/14

N2 - Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online 'TB-Profiler' tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.

AB - Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online 'TB-Profiler' tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.

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JF - Genome Medicine

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ER -

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Abstract

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