Rapid determination of antituberculosis drug resistance from wholegenome 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; M Viveiros; Isabel Portugal; Zahra Hasan; Rumina Hasan; Judith R. Glynn; Nigel Martin; Arnab Pain; Taane G. Clark

doi:https://doi.org/10.1186/s13073-015-0164-0

Rapid determination of antituberculosis drug resistance from wholegenome 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, M Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R. Glynn, Nigel Martin, Arnab Pain, Taane G. Clark

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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.

Original language	English
Journal	Genome Medicine
DOIs	https://doi.org/10.1186/s13073-015-0164-0
Publication status	Published - 2015

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Rapid determination of antituberculosis drug resistance from wholegenome sequencesFinal published version, 1.15 MBLicence: CC BY

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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 antituberculosis drug resistance from wholegenome sequences. Genome Medicine. https://doi.org/10.1186/s13073-015-0164-0

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title = "Rapid determination of antituberculosis drug resistance from wholegenome sequences.",

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 {\textquoteleft}TB-Profiler{\textquoteright} 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 M Viveiros and Isabel Portugal and Zahra Hasan and Rumina Hasan and Glynn, {Judith R.} and Nigel Martin and Arnab Pain and Clark, {Taane G.}",

year = "2015",

doi = "https://doi.org/10.1186/s13073-015-0164-0",

language = "English",

journal = "Genome Medicine",

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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 antituberculosis drug resistance from wholegenome sequences.', Genome Medicine. https://doi.org/10.1186/s13073-015-0164-0

TY - JOUR

T1 - Rapid determination of antituberculosis drug resistance from wholegenome sequences.

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, M

AU - Portugal, Isabel

AU - Hasan, Zahra

AU - Hasan, Rumina

AU - Glynn, Judith R.

AU - Martin, Nigel

AU - Pain, Arnab

AU - Clark, Taane G.

PY - 2015

Y1 - 2015

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.

U2 - https://doi.org/10.1186/s13073-015-0164-0

DO - https://doi.org/10.1186/s13073-015-0164-0

M3 - Article

JO - Genome Medicine

JF - Genome Medicine

ER -

Rapid determination of antituberculosis drug resistance from wholegenome sequences.

Abstract

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