References
- 1. World Health Organisation. Global Tuberculosis Report 2017. Geneva: WHO; 2017.
- 2. Brossier F, Guindo D, Pham A, et al. Performance of the New Version (v2.0) of the GenoType MTBDRsl Test for Detection of Resistance to Second-Line Drugs in Multidrug-Resistant Mycobacterium tuberculosis Complex Strains. J Clin Microbiol. 2016;54(6):1573-1580.
- 3. Porvaznik I, Mokry J, Solovic I. Drug resistance to anti-tuberculotics in children – three years status in Slovakia. Acta Medica Martiniana 2013, 13(3): 18-22
- 4. Dheda K, Gumbo T, Maartens G, et al. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. Lancet Respir Med. 2017;
- 5. World Health Organisation. WHO treatment guidelines for drug-resistant tuberculosis 2016 update. Geneva, Switzerland 2016
- 6. World Health Organisation. Global Tuberculosis Report 2017. Geneva: WHO; 2017.
- 7. Daley CL, Caminero JA. Management of multidrug resistant tuberculosis. Semin Respir Crit Care Med. 2013;34(1):44-59.
- 8. Lynch JB. Multidrug-resistant Tuberculosis. Med Clin North Am. 2013;97(4):553-79.
- 9. Cirillo DM, Miotto P, Tortoli E. Evolution of Phenotypic and Molecular Drug Susceptibility Testing. Adv Exp Med Biol. 2017;1019:221-246.
- 10. Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537-44.
- 11. Black PA, De vos M, Louw GE, et al. Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC Genomics. 2015;16:857.
- 12. Galagan JE. Genomic insights into tuberculosis. Nat Rev Genet. 2014;15(5):307-20.
- 13. Niemann S, Supply P. Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med. 2014;4(12):a021188.
- 14. Mukhopadhyay R. DNA sequencers: the next generation. Anal Chem. 2009;81(5):1736-40.
- 15. Anderson MW, Schrijver I. Next generation DNA sequencing and the future of genomic medicine. Genes (Basel). 2010;1(1):38-69.
- 16. Zvárová J, Mazura I. Metody molekulární biologie a bioinformatiky. 1. vyd. Praha: Karolinum, 2012. Biomedicínská informatika. ISBN 978-80-246-2150-0.
- 17. Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet. 2014;30(9):401-7.
- 18. Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530(7589):228-232.
- 19. Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. 2017;72(1):104-114.
- 20. World Health Organisation. HIV drug resistance surveillance guidance: 2015 update, Geneva 2015
- 21. Pfyffer GE, Wittwer F. Incubation time of mycobacterial cultures: how long is long enough to issue a final negative report to the clinician?. J Clin Microbiol. 2012;50(12):4188-9.
- 22. Witney AA, Cosgrove CA, Arnold A, Hinds J, Stoker NG, Butcher PD. Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med. 2016;14:46.
- 23. Almeida da silva PE, Palomino JC. Molecular basis and mechanisms of drug resistance in Myco -bacterium tuberculosis: classical and new drugs. J Antimicrob Chemother. 2011;66(7):1417–30.
- 24. Reece RJ. Analysis of Genes and Genomes. Wiley; 2004.
- 25. De vos M, Müller B, Borrell S, et al. Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob Agents Chemother. 2013;57(2):827-32.
- 26. Miotto P, Tessema B, Tagliani E, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in. Eur Respir J. 2017;50(6)
- 27. Farhat MR, Shapiro BJ, Kieser KJ, et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013;45(10):1183-9.
- 28. Zhang H, Li D, Zhao L, et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet. 2013; 45(10):1255-60.
- 29. Hoagland DT, Liu J, Lee RB, Lee RE. New agents for the treatment of drug-resistant Mycobacterium tuberculosis. Adv Drug Deliv Rev. 2016;102:55-72.
- 30. Warner DF, Koch A, Mizrahi V. Diversity and disease pathogenesis in Mycobacterium tuberculosis. Trends Microbiol. 2015;23(1):14-21.
- 31. Satta G, Lipman M, Smith GP, Arnold C, Kon OM, Mchugh TD. Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?. Clin Microbiol Infect. 2018;24(6):604-609.
- 32. Porvaznik I, Mokry J, Solovic I. Classical against molecular-genetic methods for susceptibility testing of antituberculotics. Adv Exp Med Biol. 2015,835:15-22
- 33. Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13(9):601-612.
- 34. Coll F, Mcnerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015;7(1):51.
- 35. Feuerriegel S, Schleusener V, Beckert P, et al. PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data. J Clin Microbiol. 2015;53(6):1908-14.
- 36. Parrish N, Carrol K. Importance of improved TB diagnostics in addressing the extensively drug-resistant TB crisis. Future Microbiol. 2008;3(4):405-13.
- 37. Witney AA, Gould KA, Arnold A, et al. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J Clin Microbiol. 2015;53(5):1473-83.
- 38. Rufai SB, Kumar P, Singh A, Prajapati S, Balooni V, Singh S. Comparison of Xpert MTB/RIF with line probe assay for detection of rifampin-monoresistant Mycobacterium tuberculosis. J Clin Microbiol. 2014;52(6):1846-52.
- 39. Velayati AA, Farnia P, Mozafari M, et al. High prevelance of rifampin-monoresistant tuberculosis: a retrospective analysis among Iranian pulmonary tuberculosis patients. Am J Trop Med Hyg. 2014;90(1):99-105.
- 40. US Food and Drug Administration, 2013
- 41. Walker TM, Kohl TA, Omar SV, et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis. 2015;15(10):1193-1202.
- 42. Chatterjee A, Nilgiriwala K, Saranath D, Rodrigues C, Mistry N. Whole genome sequencing of clinical strains of Mycobacterium tuberculosis from Mumbai, India: A potential tool for determining drug-resistance and strain lineage. Tuberculosis (Edinb). 2017;107:63-72.
- 43. Shea J, Halse TA, Lapierre P, et al. Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol. 2017;55(6):1871-1882.
- 44. Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ. 2014;2:e585.
- 45. Brown AC, Bryant JM, Einer-Jensen K, et al. Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples. J Clin Microbiol. 2015;53(7):2230-7.
- 46. Colman RE, Anderson J, Lemmer D, et al. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol. 2016;54(8):2058-67.
- 47. Votintseva AA, Bradley P, Pankhurst L, et al. Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples. J Clin Microbiol. 2017;55(5):1285-1298.
- 48. Nelson KN, Shah NS, Mathema B, et al. Spatial Patterns of Extensively drug-resistant Tuberculosis (XDR-tuberculosis) transmission in KwaZulu-Natal, South Africa. J Infect Dis. 2018;
- 49. Guthrie JL, Delli pizzi A, Roth D, et al. Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005-2014. J Infect Dis. 2018;218(7):1155-1163.
- 50. Sobkowiak B, Glynn JR, Houben RMGJ, et al. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics. 2018;19(1):613.
- 51. Andries K, Verhasselt P, Guillemont J, et al. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science. 2005;307(5707):223-7.
- 52. Bryant JM, Harris SR, Parkhill J, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med. 2013;1(10):786-92.