A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China—the country with the third highest tuberculosis burden—we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Data availability

Sequencing reads have been submitted to the European Nucleotide Archive (EMBL-EBI) under study accession PRJEB23157. The geographic information for individual isolates is listed in Supplementary Table 3. The analysis scripts used in this study are available online at GitHub (https://github.com/StopTB/China_TB_Evolutionary_History).

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Bos, K. I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494–497 (2014).

  2. 2.

    Global Tuberculosis Report 2017 (World Health Organization, 2017).

  3. 3.

    Narain, J. P., Raviglione, M. C. & Kochi, A. HIV-associated tuberculosis in developing countries: epidemiology and strategies for prevention. Tuber. Lung Dis. 73, 311–321 (1992).

  4. 4.

    Steffen, R., Rickenbach, M., Wilhelm, U., Helminger, A. & Schar, M. Health problems after travel to developing countries. J. Infect. Dis. 156, 84–91 (1987).

  5. 5.

    Fusegawa, H. et al. Outbreak of tuberculosis in a 2000-year-old Chinese population. Kansenshogaku Zasshi 77, 146–149 (2003).

  6. 6.

    Prasad, P. V. General medicine in Atharvaveda with special reference to Yaksma (consumption/tuberculosis). Bull. Indian Inst. Hist. Med. Hyderabad 32, 1–14 (2002).

  7. 7.

    Suzuki, T. & Inoue, T. Earliest evidence of spinal tuberculosis from the Aneolithic Yayoi period in Japan. Int. J. Osteoarchaeol. 17, 392–402 (2007).

  8. 8.

    Li, X. et al. Archaeological and palaeopathological study on the third/second century bc grave from Turfan, China: individual health history and regional implications. Quat. Int. 290, 335–343 (2013).

  9. 9.

    Packard, R. M. White Plague, Black Labor: Tuberculosis and the Political Economy of Health and Disease in South Africa (Univ. California Press, Berkeley, 1989).

  10. 10.

    Dubos, R. J. & Dubos, J. The White Plague: Tuberculosis, Man, and Society (Rutgers Univ. Press, New Brunswick, 1952).

  11. 11.

    Stead, W. W. The origin and erratic global spread of tuberculosis. How the past explains the present and is the key to the future. Clin. Chest Med. 18, 65–77 (1997).

  12. 12.

    Zhang, Z. Epidemic Chronology of Ancient China [in Chinese] (Fujian Science and Technology Press, Fuzhou, 2007).

  13. 13.

    Bates, J. H. & Stead, W. W. The history of tuberculosis as a global epidemic. Med. Clin. North Am. 77, 1205–1217 (1993).

  14. 14.

    Perry, E. J. & Selden, M. Chinese Society: Change, Conflict and Resistance (Routledge, London, 2003).

  15. 15.

    Wang, F. & Zuo, X. Inside China’s cities: institutional barriers and opportunities for urban migrants. Am. Econ. Rev. 89, 276–280 (1999).

  16. 16.

    O’Neill, M. B. et al. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Preprint at https://www.biorxiv.org/content/early/2017/10/27/210161 (2017).

  17. 17.

    Pepperell, C. S. et al. Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc. Natl Acad. Sci. USA 108, 6526–6531 (2011).

  18. 18.

    Hershberg, R. et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 6, e311 (2008).

  19. 19.

    Wirth, T. et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS. Pathog. 4, e1000160 (2008).

  20. 20.

    Gagneux, S. & Small, P. M. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect. Dis. 7, 328–337 (2007).

  21. 21.

    Stucki, D. et al. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat. Genet. 48, 1535–1543 (2016).

  22. 22.

    Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915–918 (2007).

  23. 23.

    Pepperell, C. S. et al. The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog. 9, e1003543 (2013).

  24. 24.

    Bjorn-Mortensen, K. et al. Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland. Sci. Rep. 6, 33180 (2016).

  25. 25.

    Lee, R. S. et al. Population genomics of Mycobacterium tuberculosis in the Inuit. Proc. Natl Acad. Sci. USA 112, 13609–13614 (2015).

  26. 26.

    Comas, I. et al. Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in Sub-Saharan Africa. Curr. Biol. 25, 3260–3266 (2015).

  27. 27.

    Holt, K. E. et al. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat. Genet. 50, 849–856 (2018).

  28. 28.

    Van Soolingen, D. et al. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia. J. Clin. Microbiol. 33, 3234–3238 (1995).

  29. 29.

    Pang, Y. et al. Spoligotyping and drug resistance analysis of Mycobacterium tuberculosis strains from national survey in China. PLoS ONE 7, e32976 (2012).

  30. 30.

    Coll, F. et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat. Commun. 5, 4812 (2014).

  31. 31.

    Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 45, 1176–1182 (2013).

  32. 32.

    Ge, J. China Population History (Zhongguo Renkou Shi) (Fudan Univ. Press, Shanghai, 2000).

  33. 33.

    Wang, L. et al. Tuberculosis prevalence in China, 1990–2010; a longitudinal analysis of national survey data. Lancet 383, 2057–2064 (2014).

  34. 34.

    Neher, R. A. & Hallatschek, O. Genealogies of rapidly adapting populations. Proc. Natl Acad. Sci. USA 110, 437–442 (2013).

  35. 35.

    Magiorkinis, G. et al. Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics. PLoS Comput. Biol. 9, e1002876 (2013).

  36. 36.

    Guang-Hui, H. Historical Population Geography of Beijing [in Chinese] (Peking Univ. Press, Beijing, 1996).

  37. 37.

    Hou Ren-Zhi, T. X.-F. Historical Geography of Beijing City [in Chinese] (Beijing Yanshan Press, Beijing, 2000).

  38. 38.

    Huang, Q.-S. & Yang, G.-H. The placename of immigration in Sichuan and Huguang people migrate into Sichuan. J. Southwest China Normal Univ. 3, 023 (2005).

  39. 39.

    Millward, J. A. Eurasian Crossroads: A History of Xinjiang (Columbia Univ. Press, New York, 2007).

  40. 40.

    Poston, D. L. Jr., Mao, M. X. & Yu, M.-Y. The global distribution of the overseas Chinese around 1990. Popul. Dev. Rev. 20, 631–645 (1994).

  41. 41.

    Li, P. S. The rise and fall of Chinese immigration to Canada: newcomers from Hong Kong special administrative region of China and mainland China, 1980–2000. Int. Migr. 43, 9–34 (2005).

  42. 42.

    King, H. & Locke, F. B. Chinese in the United States: a century of occupational transition. Int. Migr. Rev. 14, 15–42 (1980).

  43. 43.

    Gagneux, S. et al. Variable host–pathogen compatibility in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 103, 2869–2873 (2006).

  44. 44.

    McNeill, W. H. Human migration in historical perspective. Popul. Dev. Rev. 10, 1–18 (1984).

  45. 45.

    Gan, F. Ancient Glass Research Along the Silk Road (World Scientific, Hackensack, 2009).

  46. 46.

    Kauz, R. Aspects of the Maritime Silk Road: From the Persian Gulf to the East China Sea (Harrassowitz, Wiesbaden, 2010).

  47. 47.

    McPherson, K. China and the Maritime Silk Route. In Proc. of the UNESCO Quanzhou International Seminar on China and the Maritime Routes of the Silk Roads 55–60 (People’s Publishing House, 1991).

  48. 48.

    Lin, J. Y. The Needham puzzle: why the industrial revolution did not originate in China. Econ. Dev. Cult. Change 43, 269–292 (1995).

  49. 49.

    Jones, E. L., Frost, L. & White, C. Coming Full Circle: An Economic History of the Pacific Rim (Westview Press, Colorado, 1993).

  50. 50.

    Yusuf, S. & Saich, A. China Urbanizes: Consequences, Strategies, and Policies (World Bank, Washington DC, 2008).

  51. 51.

    Millward, J., Dunnell, R. W., Elliott, M. C. & Forêt, P. New Qing Imperial History. Making of Inner Asian Empire at Qing Chengde (RoutledgeCurzon, New York, 2004).

  52. 52.

    Mote, F. W., Twitchett, D. & Fairbank, J. K. The Cambridge History of China: Volume 7, The Ming Dynasty, 1368–1644 (Cambridge Univ. Press, London, 1988).

  53. 53.

    Yang, C. et al. Transmission of Mycobacterium tuberculosis in China: a population-based molecular epidemiologic study. Clin. Infect. Dis. 61, 219–227 (2015).

  54. 54.

    Ackley, S. F., Liu, F., Porco, T. C. & Pepperell, C. S. Modeling historical tuberculosis epidemics among Canadian First Nations: effects of malnutrition and genetic variation. PeerJ 3, e1237 (2015).

  55. 55.

    Yang, C. et al. Mycobacterium tuberculosis Beijing strains favor transmission but not drug resistance in China. Clin. Infect. Dis. 55, 1179–1187 (2012).

  56. 56.

    De Jong, B. C. et al. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J. Infect. Dis. 198, 1037–1043 (2008).

  57. 57.

    Liu, Q. et al. Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. Emerg. Microbes Infect. 5, e14 (2016).

  58. 58.

    Van Laarhoven, A. et al. Low induction of proinflammatory cytokines parallels evolutionary success of modern strains within the Mycobacterium tuberculosis Beijing genotype. Infect. Immun. 81, 3750–3756 (2013).

  59. 59.

    Ribeiro, S. C. et al. Mycobacterium tuberculosis strains of the modern sublineage of the Beijing family are more likely to display increased virulence than strains of the ancient sublineage. J. Clin. Microbiol. 52, 2615–2624 (2014).

  60. 60.

    Ates, L. S. et al. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis. Nat. Microbiol. 3, 181–188 (2018).

  61. 61.

    Kay, G. L. et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat. Commun. 6, 6717 (2015).

  62. 62.

    Wirth, T. Massive lineage replacements and cryptic outbreaks of Salmonella Typhi in eastern and southern Africa. Nat. Genet. 47, 565–567 (2015).

  63. 63.

    Wagner, D. M. et al. Yersinia pestis and the plague of Justinian 541–543 ad: a genomic analysis. Lancet Infect. Dis. 14, 319–326 (2014).

  64. 64.

    Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).

  65. 65.

    Vagene, A. J. et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat. Ecol. Evol. 2, 520–528 (2018).

  66. 66.

    Zhao, Y. et al. National survey of drug-resistant tuberculosis in China. N. Engl. J. Med. 366, 2161–2170 (2012).

  67. 67.

    Liu, Q., Luo, T., Li, J., Mei, J. & Gao, Q. Triplex real-time PCR melting curve analysis for detecting Mycobacterium tuberculosis mutations associated with resistance to second-line drugs in a single reaction. J. Antimicrob. Chemother. 68, 1097–1103 (2013).

  68. 68.

    Farhat, M. R. et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet. 45, 1183–1189 (2013).

  69. 69.

    Comas, I., Homolka, S., Niemann, S. & Gagneux, S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS ONE 4, e7815 (2009).

  70. 70.

    Luo, T. et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc. Natl Acad. Sci. USA 112, 8136–8141 (2015).

  71. 71.

    Merker, M. et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat. Genet. 47, 242–249 (2015).

  72. 72.

    Barbier, M. & Wirth, T. The evolutionary history, demography, and spread of the Mycobacterium tuberculosis complex. Microbiol. Spectr. 4, TBTB2-0008-2016 (2016).

  73. 73.

    Brudey, K. et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6, 23 (2006).

  74. 74.

    Viegas, S. O. et al. Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mozambique. BMC Microbiol. 10, 195 (2010).

  75. 75.

    Zhang, H. et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat. Genet. 45, 1255–1260 (2013).

  76. 76.

    Joshi, N. A. & Fass, J. N. Sickle: A Sliding-Window, Adaptive, Quality-Based Trimming Tool for FastQ Files (2011); https://github.com/najoshi/sickle

  77. 77.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  78. 78.

    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

  79. 79.

    Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).

  80. 80.

    Gan, M., Liu, Q., Yang, C., Gao, Q. & Luo, T. Deep whole-genome sequencing to detect mixed infection of Mycobacterium tuberculosis. PLoS ONE 11, e0159029 (2016).

  81. 81.

    Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

  82. 82.

    Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).

  83. 83.

    RStudio Team RStudio: Integrated Development for R (RStudio, 2015).

  84. 84.

    Paradis, E. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419–420 (2010).

  85. 85.

    Hsieh, T., Ma, K. & Chao, A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol. Evol. 7, 1451–1456 (2016).

  86. 86.

    Yu, Y., Harris, A. J., Blair, C. & He, X. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Mol. Phylogenet. Evol. 87, 46–49 (2015).

  87. 87.

    Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).

  88. 88.

    Gignoux, C. R., Henn, B. M. & Mountain, J. L. Rapid, global demographic expansions after the origins of agriculture. Proc. Natl Acad. Sci. USA 108, 6044–6049 (2011).

Download references


We thank T. M. Walker for sharing the geographic information of 3,651 MTBC isolates of multiple continents origin. We also thank Y.-X. Fu and X. Liu for advice on effective population size calculation and fruitful discussions, and D. Brites and C. Wang for help with clarifying technical details of data analysis during this work. This work was supported by the Natural Science Foundation of China (91631301 and 81661128043 to Q.G. and 81701975 to Q.L.). C.S.P. was supported by the National Institutes of Health (grant 1R01AI113287-01A1). S.G. was supported by the Swiss National Science Foundation (grants IZRJZ3_164171, 310030_166687, IZLSZ3_170834 and CRSII5_177163). This work was also supported by MINECO research grant SAF2016-77346-R (to I.C.), the European Research Council (638553-TB-ACCELERATE to I.C.), the National Science and Technology Major Project of China (2017ZX10201302 to Q.G., 2018ZX10103001 to Y.Z.), the Sanming Project of Medicine in Shenzhen (SZSM201611030 to Q.G.), JSGG20170413142559220 (to Q.G.), and National Basic Research programme of China (2014CB744403 to Y.Z.).

Author information

Author notes

  1. These authors contributed equally: Aijing Ma, Lanhai Wei.


  1. Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China

    • Qingyun Liu
    • , Qi Jiang
    • , Mingyu Gan
    • , Tianyu Zuo
    • , Mei Liu
    • , Chongguang Yang
    •  & Qian Gao
  2. Shenzhen Center for Chronic Disease Control, Shenzhen, China

    • Qingyun Liu
    • , Qi Jiang
    • , Mingyu Gan
    •  & Qian Gao
  3. National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China

    • Aijing Ma
    • , Yang Zhou
    •  & Yanlin Zhao
  4. State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China

    • Lanhai Wei
    • , Hong-Xiang Zheng
    •  & Li Jin
  5. National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China

    • Yu Pang
  6. The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China

    • Beibei Wu
  7. West China School of Basic Medical Sciences and Forensic Medicines, Sichuan University, Chengdu, China

    • Tao Luo
  8. Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA

    • Chongguang Yang
  9. Institute of Biomedicine of Valencia, CSIC and CIBER in Epidemiology and Public Health, Valencia, Spain

    • Iñaki Comas
  10. Swiss Tropical and Public Health Institute, Basel, Switzerland

    • Sebastien Gagneux
  11. University of Basel, Basel, Switzerland

    • Sebastien Gagneux
  12. Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA

    • Caitlin S. Pepperell
  13. Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA

    • Caitlin S. Pepperell


  1. Search for Qingyun Liu in:

  2. Search for Aijing Ma in:

  3. Search for Lanhai Wei in:

  4. Search for Yu Pang in:

  5. Search for Beibei Wu in:

  6. Search for Tao Luo in:

  7. Search for Yang Zhou in:

  8. Search for Hong-Xiang Zheng in:

  9. Search for Qi Jiang in:

  10. Search for Mingyu Gan in:

  11. Search for Tianyu Zuo in:

  12. Search for Mei Liu in:

  13. Search for Chongguang Yang in:

  14. Search for Li Jin in:

  15. Search for Iñaki Comas in:

  16. Search for Sebastien Gagneux in:

  17. Search for Yanlin Zhao in:

  18. Search for Caitlin S. Pepperell in:

  19. Search for Qian Gao in:


Q.L., Y.Z., C.S.P. and Q.G. designed and implemented the study. Y.P., B.W., Y.Z. and Q.G. collected and contributed the MTBC isolates analysed in this study. Q.L., A.M. and Y.Z. conducted the SNP genotyping work. M.L. and C.Y. conducted the MIRU-VNTR typing and analysis. Q.L., T.L., M.G. and T.Z. analysed the sequencing reads and performed the genetic analysis. L.W., H.-X.Z. and L.J. participated in the analysis of integrating tuberculosis history with Chinese human population history. Q.J. performed the statistical analysis. Q.L., I.C., S.G., C.S.P. and Q.G. drafted the manuscript. All authors critically reviewed and approved the final version of the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Yanlin Zhao or Caitlin S. Pepperell or Qian Gao.

Supplementary Information

  1. Supplementary Information

    Supplementary figures 1–11, supplementary tables 1–7 and supplementary discussion

  2. Reporting Summary

About this article

Publication history




Issue Date



Further reading