Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data

Bioinformatics

Volumn 34, Issue 10, 2018, Pages 1666-1671

  Yang, Yang ^a   Niehaus, Katherine E ^a   Walker, Timothy M ^b   Iqbal, Zamin ^b   Walker, A Sarah ^b,c   Wilson, Daniel J ^b   Peto, Tim E A ^b,d   Crook, Derrick W ^b,c,d   Smith, E Grace ^d   Zhu, Tingting ^a   Clifton, David A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

^d PUBLIC HEALTH ENGLAND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CIPROFLOXACIN; ETHAMBUTOL; ISONIAZID; MOXIFLOXACIN; OFLOXACIN; PYRAZINAMIDE; RIFAMPICIN; STREPTOMYCIN; TUBERCULOSTATIC AGENT;

CLASSIFICATION; DNA SEQUENCE; GENETICS; HUMAN; MACHINE LEARNING; MICROBIAL SENSITIVITY TEST; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; PROCEDURES;

ANTITUBERCULAR AGENTS; CIPROFLOXACIN; ETHAMBUTOL; HUMANS; ISONIAZID; MACHINE LEARNING; MICROBIAL SENSITIVITY TESTS; MOXIFLOXACIN; MYCOBACTERIUM TUBERCULOSIS; OFLOXACIN; PYRAZINAMIDE; RIFAMPIN; SEQUENCE ANALYSIS, DNA; STREPTOMYCIN; TUBERCULOSIS, MULTIDRUG-RESISTANT;

EID: 85047073629     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx801     Document Type: Article

References (17)

1. Ando, H. et al. (2014) A silent mutation in maba confers isoniazid resistance on Mycobacterium tuberculosis. Mol. Microbiol., 91, 538-547.
2. Benavente, E. D. et al. (2015) Phytb: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16, 155.
3. Casali, N. et al. (2014) Evolution and transmission of drug resistant tuberculosis in a Russian population. Nat. Genet., 46, 279.
4. Cohen, K. A. et al. (2015) Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLoS Med., 12, e1001880.
5. Coll, F. et al. (2015) Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med., 7, 1.
6. Comas, I. et al. (2011) Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in rna polymerase genes. Nat. Genet., 44, 106-110.
7. Eldholm, V. et al. (2016) Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA, 113, 13881-13886.
8. Farhat, M. R. et al. (2013) Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet., 45, 1183-1189.
9. Feuerriegel, S. et al. (2014) Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex. J. Antimicrob. Chemother., 69, 1205-1210.
10. Ford, C. B. et al. (2013) Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat. Genet., 45, 784-790.
11. Georghiou, S. B. et al. (2012) Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: a systematic review. PloS One, 7, e33275.
12. Global tuberculosis report (2017). Geneva: World Health Organization. Licence: CC BY-NC-SA 3. 0 IGO.
13. Safi, H. et al. (2013) Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-[beta]-d-arabinose biosynthetic and utilization pathway genes. Nat. Genet., 45, 1190-1197.
14. Stucki, D. et al. (2012) Two new rapid snp-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One, 7, e41253.
15. Walker, T. M. et al. (2015) Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect. Dis., 15, 1193-1202.
16. WHO treatment guidelines for drug-resistant tuberculosis (2016 update). (2016). Geneva: World Health Organization.
17. Zhang, H. et al. (2013) Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat. Genet., 45, 1255-1260.