- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, Guangxi 530028, P. R. China;
ZHOU Chongxing,
Email: 86501629@qq.com
Mycobacterium tuberculosis is the causative agent of human tuberculosis. Through the genotyping of Mycobacterium tuberculosis, we can find the epidemic situation and characteristics of tuberculosis in time, analyze the transmission chain between patients in different jurisdictions, and formulate effective intervention measures in time, to provide a strong basis for clinical diagnosis and treatment. At present, several genotyping techniques for Mycobacterium tuberculosis have their advantages and disadvantages in application. This article reviews the genotyping technology, population genetics and genotyping naming rules of Mycobacterium tuberculosis.
Citation： ZHOU Chongxing. Genotyping and naming rules of Mycobacterium tuberculosis. West China Medical Journal, 2022, 37(11): 1742-1748. doi: 10.7507/1002-0179.202110045 Copy
Copyright © the editorial department of West China Medical Journal of West China Medical Publisher. All rights reserved
| 1. | Mathema B, Kurepina NE, Bifani PJ, et al. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev, 2006, 19(4): 658-685. |
| 2. | Collins DM, De Lisle GW. DNA restriction endonuclease analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG. J Gen Microbiol, 1984, 130(4): 1019-1021. |
| 3. | Zhang Y, Mazurek GH, Cave MD, et al. DNA polymorphisms in strains of Mycobacterium tuberculosis analyzed by pulsed-field gel electrophoresis: a tool for epidemiology. J Clin Microbiol, 1992, 30(6): 1551-1556. |
| 4. | Cave MD, Eisenach KD, McDermott PF, et al. IS6110: conservation of sequence in the Mycobacterium tuberculosis complex and its utilization in DNA fingerprinting. Mol Cell Probes, 1991, 5(1): 73-80. |
| 5. | van Soolingen D, Hermans PW, de Haas PE, et al. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol, 1991, 29(11): 2578-2586. |
| 6. | Asgharzadeh M, Kafil HS. Current trends in molecular epidemiology studies of Mycobacterium tuberculosis. Biotechnol Mol Biol Rev, 2007, 2(5): 108. |
| 7. | Behr MA, Wilson MA, Gill WP, et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science, 1999, 284(5419): 1520-1523. |
| 8. | Brosch R, Gordon SV, Marmiesse M, et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A, 2002, 99(6): 3684-3689. |
| 9. | Mazars E, Lesjean S, Banuls AL, et al. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A, 2001, 98(4): 1901-1906. |
| 10. | Allix-Béguec C, Harmsen D, Weniger T, et al. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2008, 46(8): 2692-2699. |
| 11. | Coll F, McNerney R, Guerra-Assunção JA, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun, 2014, 5(9): 4812. |
| 12. | Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437(7057): 376-380. |
| 13. | Kohl TA, Diel R, Harmsen D, et al. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol, 2014, 52(7): 2479-2486. |
| 14. | Kohl TA, Harmsen D, Rothgänger J, et al. Harmonized genome wide typing of tubercle bacilli using a web-based gene-by-gene nomenclature system. EBioMedicine, 2018, 34(8): 131-138. |
| 15. | van der Werf MJ, Ködmön C. Whole-genome sequencing as tool for investigating international tuberculosis outbreaks: a systematic review. Front Public Health, 2019, 7: 87. |
| 16. | Meehan CJ, Goig GA, Kohl TA, et al. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol, 2019, 17(9): 533-545. |
| 17. | Pitondo-Silva A, Santos AC, Jolley KA, et al. Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis. J Microbiol Methods, 2013, 93(1): 42-48. |
| 18. | O’Neill MB, Shockey A, Zarley A, et al. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol, 2019, 28(13): 3241-3256. |
| 19. | van Soolingen D, Qian L, de Haas PE, et al. Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J Clin Microbiol, 1995, 33(12): 3234-3238. |
| 20. | Parwati I, van Crevel R, van Soolingen D. Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains. Lancet Infect Dis, 2010, 10(2): 103-111. |
| 21. | Chan MY, Borgdorff M, Yip CW, et al. Seventy percent of the Mycobacterium tuberculosis isolates in Hong Kong represent the Beijing genotype. Epidemiol Infect, 2001, 127(1): 169-171. |
| 22. | Kremer K, van-der-Werf MJ, Au BK, et al. Vaccine-induced immunity circumvented by typical Mycobacterium tuberculosis Beijing strains. Emerg Infect Dis, 2009, 15(2): 335-339. |
| 23. | Sreevatsan S, Pan X, Stockbauer KE, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A, 1997, 94(18): 9869-9874. |
| 24. | Baker LV, Brown TJ, Maxwell O, et al. Molecular analysis of isoniazid-resistant Mycobacterium tuberculosis isolates from England and Wales reveals the phylogenetic significance of the ahpC -46A polymorphism. Antimicrob Agents Chemother, 2005, 49(4): 1455-1464. |
| 25. | Gagneux S, DeRiemer K, Van T, et al. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A, 2006, 103(8): 2869-2873. |
| 26. | Gutacker MM, Mathema B, Soini H, et al. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. J Infect Dis, 2006, 193(1): 121-128. |
| 27. | Filliol I, Driscoll JR, van Soolingen D, et al. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol, 2003, 41(5): 1963-1970. |
| 28. | Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis, 2007, 7(5): 328-337. |
| 29. | Firdessa R, Berg S, Hailu E, et al. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis, 2013, 19(3): 460-463. |
| 30. | Ngabonziza JCS, Loiseau C, Marceau M, et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun, 2020, 11(1): 2917. |
| 31. | Meehan CJ, Moris P, Kohl TA, et al. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine, 2018, 37(11): 410-416. |
| 32. | Ravansalar H, Tadayon K, Ghazvini K. Molecular typing methods used in studies of Mycobacterium tuberculosis in Iran: a systematic review. Iran J Microbiol, 2016, 8(5): 338-346. |
| 33. | Joshi KR, Dhiman H, Scaria V. tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. Database (Oxford), 2014, 2014(1): t83. |
| 34. | 张洁, 任怡宣, 潘丽萍, 等. 全基因组测序在结核分枝杆菌研究中的应用. 中国防痨杂志, 2020, 42(7): 737-740. |
| 35. | Mahairas GG, Sabo PJ, Hickey MJ, et al. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol, 1996, 178(5): 1274-1282. |
| 36. | Brudey K, Driscoll JR, Rigouts L, et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol, 2006, 6(3): 23. |
| 37. | Dale JW, Brittain D, Cataldi AA, et al. Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature. Int J Tuberc Lung Dis, 2001, 5(3): 216-219. |
| 38. | Weniger T, Krawczyk J, Supply P, et al. MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. Nucleic Acids Res, 2010, 38(Web Server issue): W326-331. |
| 39. | Tang C, Reyes JF, Luciani F, et al. spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex. Bioinformatics, 2008, 24(20): 2414-2415. |
| 40. | Shabbeer A, Cowan LS, Ozcaglar C, et al. TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex. Infect Genet Evol, 2012, 12(4): 789-797. |
| 41. | Demay C, Liens B, Burguière T, et al. SITVITWEB-a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol, 2012, 12(4): 755-766. |
| 42. | Couvin D, David A, Zozio T, et al. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect Genet Evol, 2019, 72(8): 31-43. |
| 43. | Rodriguez-Campos S, González S, de Juan L, et al. A database for animal tuberculosis (mycoDB. es) within the context of the Spanish national programme for eradication of bovine tuberculosis. Infect Genet Evol, 2012, 12(4): 877-882. |
| 44. | Smith NH, Upton P. Naming spoligotype patterns for the RD9-deleted lineage of the Mycobacterium tuberculosis complex; www. Mbovis. org. Infect Genet Evol, 2012, 12(4): 873-876. |
| 45. | Soares P, Alves RJ, Abecasis AB, et al. inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. BMC Bioinformatics, 2013, 14(8): 264. |
| 46. | Coll F, Preston M, Guerra-Assunção JA, et al. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb), 2014, 94(3): 346-354. |
| 47. | Chernyaeva EN, Shulgina MV, Rotkevich MS, et al. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics, 2014, 15(4): 308. |
| 48. | 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. |
| 49. | 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): 1908-1914. |
| 50. | Sekizuka T, Yamashita A, Murase Y, et al. TGS-TB: total genotyping solution for Mycobacterium tuberculosis using short-read whole-genome sequencing. PLoS One, 2015, 10(11): e142951. |
| 51. | Iwai H, Kato-Miyazawa M, Kirikae T, et al. CASTB (the comprehensive analysis server for the Mycobacterium tuberculosis complex): a publicly accessible web server for epidemiological analyses, drug-resistance prediction and phylogenetic comparison of clinical isolates. Tuberculosis (Edinb), 2015, 95(6): 843-844. |
| 52. | Perdigão J, Silva C, Diniz J, et al. Clonal expansion across the seas as seen through CPLP-TB database: a joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. Infect Genet Evol, 2019, 72(8): 44-58. |
| 53. | Tornheim JA, Starks AM, Rodwell TC, et al. Building the framework for standardized clinical laboratory reporting of next-generation sequencing data for resistance-associated mutations in Mycobacterium tuberculosis complex. Clin Infect Dis, 2019, 69(9): 1631-1633. |
- 1. Mathema B, Kurepina NE, Bifani PJ, et al. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev, 2006, 19(4): 658-685.
- 2. Collins DM, De Lisle GW. DNA restriction endonuclease analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG. J Gen Microbiol, 1984, 130(4): 1019-1021.
- 3. Zhang Y, Mazurek GH, Cave MD, et al. DNA polymorphisms in strains of Mycobacterium tuberculosis analyzed by pulsed-field gel electrophoresis: a tool for epidemiology. J Clin Microbiol, 1992, 30(6): 1551-1556.
- 4. Cave MD, Eisenach KD, McDermott PF, et al. IS6110: conservation of sequence in the Mycobacterium tuberculosis complex and its utilization in DNA fingerprinting. Mol Cell Probes, 1991, 5(1): 73-80.
- 5. van Soolingen D, Hermans PW, de Haas PE, et al. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol, 1991, 29(11): 2578-2586.
- 6. Asgharzadeh M, Kafil HS. Current trends in molecular epidemiology studies of Mycobacterium tuberculosis. Biotechnol Mol Biol Rev, 2007, 2(5): 108.
- 7. Behr MA, Wilson MA, Gill WP, et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science, 1999, 284(5419): 1520-1523.
- 8. Brosch R, Gordon SV, Marmiesse M, et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A, 2002, 99(6): 3684-3689.
- 9. Mazars E, Lesjean S, Banuls AL, et al. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A, 2001, 98(4): 1901-1906.
- 10. Allix-Béguec C, Harmsen D, Weniger T, et al. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol, 2008, 46(8): 2692-2699.
- 11. Coll F, McNerney R, Guerra-Assunção JA, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun, 2014, 5(9): 4812.
- 12. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437(7057): 376-380.
- 13. Kohl TA, Diel R, Harmsen D, et al. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol, 2014, 52(7): 2479-2486.
- 14. Kohl TA, Harmsen D, Rothgänger J, et al. Harmonized genome wide typing of tubercle bacilli using a web-based gene-by-gene nomenclature system. EBioMedicine, 2018, 34(8): 131-138.
- 15. van der Werf MJ, Ködmön C. Whole-genome sequencing as tool for investigating international tuberculosis outbreaks: a systematic review. Front Public Health, 2019, 7: 87.
- 16. Meehan CJ, Goig GA, Kohl TA, et al. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol, 2019, 17(9): 533-545.
- 17. Pitondo-Silva A, Santos AC, Jolley KA, et al. Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis. J Microbiol Methods, 2013, 93(1): 42-48.
- 18. O’Neill MB, Shockey A, Zarley A, et al. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol, 2019, 28(13): 3241-3256.
- 19. van Soolingen D, Qian L, de Haas PE, et al. Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J Clin Microbiol, 1995, 33(12): 3234-3238.
- 20. Parwati I, van Crevel R, van Soolingen D. Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains. Lancet Infect Dis, 2010, 10(2): 103-111.
- 21. Chan MY, Borgdorff M, Yip CW, et al. Seventy percent of the Mycobacterium tuberculosis isolates in Hong Kong represent the Beijing genotype. Epidemiol Infect, 2001, 127(1): 169-171.
- 22. Kremer K, van-der-Werf MJ, Au BK, et al. Vaccine-induced immunity circumvented by typical Mycobacterium tuberculosis Beijing strains. Emerg Infect Dis, 2009, 15(2): 335-339.
- 23. Sreevatsan S, Pan X, Stockbauer KE, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A, 1997, 94(18): 9869-9874.
- 24. Baker LV, Brown TJ, Maxwell O, et al. Molecular analysis of isoniazid-resistant Mycobacterium tuberculosis isolates from England and Wales reveals the phylogenetic significance of the ahpC -46A polymorphism. Antimicrob Agents Chemother, 2005, 49(4): 1455-1464.
- 25. Gagneux S, DeRiemer K, Van T, et al. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A, 2006, 103(8): 2869-2873.
- 26. Gutacker MM, Mathema B, Soini H, et al. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. J Infect Dis, 2006, 193(1): 121-128.
- 27. Filliol I, Driscoll JR, van Soolingen D, et al. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol, 2003, 41(5): 1963-1970.
- 28. Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis, 2007, 7(5): 328-337.
- 29. Firdessa R, Berg S, Hailu E, et al. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis, 2013, 19(3): 460-463.
- 30. Ngabonziza JCS, Loiseau C, Marceau M, et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun, 2020, 11(1): 2917.
- 31. Meehan CJ, Moris P, Kohl TA, et al. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine, 2018, 37(11): 410-416.
- 32. Ravansalar H, Tadayon K, Ghazvini K. Molecular typing methods used in studies of Mycobacterium tuberculosis in Iran: a systematic review. Iran J Microbiol, 2016, 8(5): 338-346.
- 33. Joshi KR, Dhiman H, Scaria V. tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. Database (Oxford), 2014, 2014(1): t83.
- 34. 张洁, 任怡宣, 潘丽萍, 等. 全基因组测序在结核分枝杆菌研究中的应用. 中国防痨杂志, 2020, 42(7): 737-740.
- 35. Mahairas GG, Sabo PJ, Hickey MJ, et al. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol, 1996, 178(5): 1274-1282.
- 36. Brudey K, Driscoll JR, Rigouts L, et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol, 2006, 6(3): 23.
- 37. Dale JW, Brittain D, Cataldi AA, et al. Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature. Int J Tuberc Lung Dis, 2001, 5(3): 216-219.
- 38. Weniger T, Krawczyk J, Supply P, et al. MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. Nucleic Acids Res, 2010, 38(Web Server issue): W326-331.
- 39. Tang C, Reyes JF, Luciani F, et al. spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex. Bioinformatics, 2008, 24(20): 2414-2415.
- 40. Shabbeer A, Cowan LS, Ozcaglar C, et al. TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex. Infect Genet Evol, 2012, 12(4): 789-797.
- 41. Demay C, Liens B, Burguière T, et al. SITVITWEB-a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol, 2012, 12(4): 755-766.
- 42. Couvin D, David A, Zozio T, et al. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect Genet Evol, 2019, 72(8): 31-43.
- 43. Rodriguez-Campos S, González S, de Juan L, et al. A database for animal tuberculosis (mycoDB. es) within the context of the Spanish national programme for eradication of bovine tuberculosis. Infect Genet Evol, 2012, 12(4): 877-882.
- 44. Smith NH, Upton P. Naming spoligotype patterns for the RD9-deleted lineage of the Mycobacterium tuberculosis complex; www. Mbovis. org. Infect Genet Evol, 2012, 12(4): 873-876.
- 45. Soares P, Alves RJ, Abecasis AB, et al. inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis. BMC Bioinformatics, 2013, 14(8): 264.
- 46. Coll F, Preston M, Guerra-Assunção JA, et al. PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb), 2014, 94(3): 346-354.
- 47. Chernyaeva EN, Shulgina MV, Rotkevich MS, et al. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics, 2014, 15(4): 308.
- 48. 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.
- 49. 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): 1908-1914.
- 50. Sekizuka T, Yamashita A, Murase Y, et al. TGS-TB: total genotyping solution for Mycobacterium tuberculosis using short-read whole-genome sequencing. PLoS One, 2015, 10(11): e142951.
- 51. Iwai H, Kato-Miyazawa M, Kirikae T, et al. CASTB (the comprehensive analysis server for the Mycobacterium tuberculosis complex): a publicly accessible web server for epidemiological analyses, drug-resistance prediction and phylogenetic comparison of clinical isolates. Tuberculosis (Edinb), 2015, 95(6): 843-844.
- 52. Perdigão J, Silva C, Diniz J, et al. Clonal expansion across the seas as seen through CPLP-TB database: a joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. Infect Genet Evol, 2019, 72(8): 44-58.
- 53. Tornheim JA, Starks AM, Rodwell TC, et al. Building the framework for standardized clinical laboratory reporting of next-generation sequencing data for resistance-associated mutations in Mycobacterium tuberculosis complex. Clin Infect Dis, 2019, 69(9): 1631-1633.