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Annual Review of Genomics and Human Genetics

Volume 25, 2024

Genomic Interactions Between and Humans

Abstract

is considered by many to be the deadliest microbe, with the estimated annual cases numbering more than 10 million. The bacteria, including , are classified into nine major lineages and hundreds of sublineages, each with different geographical distributions and levels of virulence. The phylogeographic patterns can be a result of recent and early human migrations as well as coevolution between the bacteria and various human populations, which may explain why many studies on human genetic factors contributing to tuberculosis have not been replicable in different areas. Moreover, several studies have revealed the significance of interactions between human genetic variations and bacterial genotypes in determining the development of tuberculosis, suggesting coadaptation. The increased availability of whole-genome sequence data from both humans and bacteria has enabled a better understanding of these interactions, which can inform the development of vaccines and other control measures.

Keyword(s): coevolution, genome, genotypes, human genetics, Mycobacterium tuberculosis, phylogeography, risk factor, SNPs
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/content/journals/10.1146/annurev-genom-021623-101844
2024-08-27
2024-10-14
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Literature Cited

  1. 1.
    Abel L, El-Baghdadi J, Bousfiha AA, Casanova JL, Schurr E. 2014.. Human genetics of tuberculosis: a long and winding road. . Philos. Trans. R. Soc. B 369::20130428
     [Crossref] [Google Scholar]
  2. 2.
    Aiewsakun P, Katzourakis A. 2015.. Endogenous viruses: connecting recent and ancient viral evolution. . Virology 479–80::26–37
     [Crossref] [Google Scholar]
  3. 3.
    Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, et al. 2019.. A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. . Sci. Rep. 9::13718
     [Crossref] [Google Scholar]
  4. 4.
    Ajayi T, Rai P, Shi M, Gabor KA, Karmaus PWF, et al. 2023.. Race-specific association of an IRGM risk allele with cytokine expression in human subjects. . Sci. Rep. 13::12911
     [Crossref] [Google Scholar]
  5. 5.
    Asante-Poku A, Morgan P, Osei-Wusu S, Aboagye SY, Asare P, et al. 2021.. Genetic analysis of TB susceptibility variants in Ghana reveals candidate protective loci in SORBS2 and SCL11A1 genes. . Front. Genet. 12::729737
     [Crossref] [Google Scholar]
  6. 6.
    Ates LS. 2020.. New insights into the mycobacterial PE and PPE proteins provide a framework for future research. . Mol. Microbiol. 113::4–21
     [Crossref] [Google Scholar]
  7. 7.
    Bagcchi S. 2023.. WHO's Global Tuberculosis Report 2022. . Lancet Microbe 4::e20
     [Crossref] [Google Scholar]
  8. 8.
    Bainomugisa A, Lavu E, Pandey S, Majumdar S, Banamu J, et al. 2022.. Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea. . BMC Infect. Dis. 22::437
     [Crossref] [Google Scholar]
  9. 9.
    Bainomugisa A, Meumann EM, Rajahram GS, Ong RT, Coin L, et al. 2021.. Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses. . Microb. Genom. 7::000573
     [Google Scholar]
  10. 10.
    Barbier M, Dumitrescu O, Pichat C, Carret G, Ronnaux-Baron AS, et al. 2018.. Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France. . Sci. Rep. 8::5855
     [Crossref] [Google Scholar]
  11. 11.
    Barnes I, Duda A, Pybus OG, Thomas MG. 2011.. Ancient urbanization predicts genetic resistance to tuberculosis. . Evolution 65::842–48
     [Crossref] [Google Scholar]
  12. 12.
    Barreiro LB, Neyrolles O, Babb CL, Tailleux L, Quach H, et al. 2006.. Promoter variation in the DC-SIGN-encoding gene CD209 is associated with tuberculosis. . PLOS Med. 3::e20
     [Crossref] [Google Scholar]
  13. 13.
    Bespiatykh D, Bespyatykh J, Mokrousov I, Shitikov E. 2021.. A comprehensive map of Mycobacterium tuberculosis complex regions of difference. . mSphere 6::e0053521
     [Crossref] [Google Scholar]
  14. 14.
    Boisson-Dupuis S. 2020.. The monogenic basis of human tuberculosis. . Hum. Genet. 139::1001–9
     [Crossref] [Google Scholar]
  15. 15.
    Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, et al. 2014.. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. . Nature 514::494–97
     [Crossref] [Google Scholar]
  16. 16.
    Bottai D, Frigui W, Sayes F, Di Luca M, Spadoni D, et al. 2020.. TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages. . Nat. Commun. 11::684
     [Crossref] [Google Scholar]
  17. 17.
    Bowdish DM, Sakamoto K, Kim MJ, Kroos M, Mukhopadhyay S, et al. 2009.. MARCO, TLR2, and CD14 are required for macrophage cytokine responses to mycobacterial trehalose dimycolate and Mycobacterium tuberculosis. . PLOS Pathog. 5::e1000474
     [Crossref] [Google Scholar]
  18. 18.
    Bowdish DM, Sakamoto K, Lack NA, Hill PC, Sirugo G, et al. 2013.. Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population. . BMC Med. Genet. 14::47
     [Crossref] [Google Scholar]
  19. 19.
    Brites D, Gagneux S. 2017.. The nature and evolution of genomic diversity in the Mycobacterium tuberculosis complex. . In Strain Variation in the Mycobacterium tuberculosis Complex: Its Role in Biology, Epidemiology and Control, ed. S Gagneux , pp. 1–26. Cham, Switz:.: Springer
     [Google Scholar]
  20. 20.
    Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, et al. 2018.. A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. . Front. Microbiol. 9::2820
     [Crossref] [Google Scholar]
  21. 21.
    Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, et al. 2002.. A new evolutionary scenario for the Mycobacterium tuberculosis complex. . PNAS 99::3684–89
     [Crossref] [Google Scholar]
  22. 22.
    Cao W, Luo LL, Chen WW, Liang L, Zhang RR, et al. 2019.. Polymorphism in the EREG gene confers susceptibility to tuberculosis. . BMC Med. Genet. 20::7
     [Crossref] [Google Scholar]
  23. 23.
    Casadevall A, Pirofski LA. 2000.. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. . Infect. Immun. 68::6511–18
     [Crossref] [Google Scholar]
  24. 24.
    Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NT, et al. 2008.. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. . PLOS Pathog. 4::e1000034
     [Crossref] [Google Scholar]
  25. 25.
    Chen J, Ruan Q, Shen Y, Wang S, Shao L, Zhang W. 2018.. Assessing and screening for T-cell epitopes from Mycobacterium tuberculosis RD2 proteins for the diagnosis of active tuberculosis. . Braz. J. Infect. Dis. 22::462–71
     [Crossref] [Google Scholar]
  26. 26.
    Chen Y, Zeng Y, Wang J, Meng C. 2022.. Immune and inflammation-related gene polymorphisms and susceptibility to tuberculosis in Southern Xinjiang population: a case-control analysis. . Int. J. Immunogenet. 49::70–82
     [Crossref] [Google Scholar]
  27. 27.
    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. 1998.. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. . Nature 393::537–44
     [Crossref] [Google Scholar]
  28. 28.
    Coll F, McNerney R, Guerra-Assuncao JA, Glynn JR, Perdigao J, et al. 2014.. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. . Nat. Commun. 5::4812
     [Crossref] [Google Scholar]
  29. 29.
    Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, et al. 2010.. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. . Nat. Genet. 42::498–503
     [Crossref] [Google Scholar]
  30. 30.
    Comas I, Coscolla M, Luo T, Borrell S, Holt KE, et al. 2013.. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. . Nat. Genet. 45::1176–82
     [Crossref] [Google Scholar]
  31. 31.
    Comas I, Hailu E, Kiros T, Bekele S, Mekonnen W, et al. 2015.. Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in Sub-Saharan Africa. . Curr. Biol. 25::3260–66
     [Crossref] [Google Scholar]
  32. 32.
    Comstock GW. 1978.. Tuberculosis in twins: a re-analysis of the Prophit survey. . Am. Rev. Respir. Dis. 117::621–24
     [Google Scholar]
  33. 33.
    Coscolla M. 2017.. Biological and epidemiological consequences of MTBC diversity. . In Strain Variation in the Mycobacterium tuberculosis Complex: Its Role in Biology, Epidemiology and Control, ed. S Gagneux , pp. 95–116. Cham, Switz:.: Springer
     [Google Scholar]
  34. 34.
    Coscolla M, Gagneux S. 2014.. Consequences of genomic diversity in Mycobacterium tuberculosis. . Semin. Immunol. 26::431–44
     [Crossref] [Google Scholar]
  35. 35.
    Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, et al. 2021.. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. . Microb. Genom. 7::000477
     [Google Scholar]
  36. 36.
    Cummins SL. 1929.. “Virgin soil”—and after. A working conception of tuberculosis in children, adolescents, and aborigines. . Br. Med. J. 2:(3575):39–41
     [Crossref] [Google Scholar]
  37. 37.
    Daley CL, Small PM, Schecter GF, Schoolnik GK, McAdam RA, et al. 1992.. An outbreak of tuberculosis with accelerated progression among persons infected with the human immunodeficiency virus: an analysis using restriction-fragment–length polymorphisms. . N. Engl. J. Med. 326::231–35
     [Crossref] [Google Scholar]
  38. 38.
    Das J, Banday AZ, Shandilya J, Sharma M, Vignesh P, Rawat A. 2021.. An updated review on Mendelian susceptibility to mycobacterial diseases—a silver jubilee celebration of its first genetic diagnosis. . Expert Rev. Clin. Immunol. 17::1103–20
     [Crossref] [Google Scholar]
  39. 39.
    de Jong BC, Antonio M, Gagneux S. 2010.. Mycobacterium africanum—review of an important cause of human tuberculosis in West Africa. . PLOS Negl. Trop. Dis. 4::e744
     [Crossref] [Google Scholar]
  40. 40.
    Demay C, Liens B, Burguiere T, Hill V, Couvin D, et al. 2012.. SITVITWEB—a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. . Infect. Genet. Evol. 12::755–66
     [Crossref] [Google Scholar]
  41. 41.
    Di Pietrantonio T, Schurr E. 2013.. Host-pathogen specificity in tuberculosis. . In The New Paradigm of Immunity to Tuberculosis, ed. M Divangahi , pp. 33–44. New York:: Springer
     [Google Scholar]
  42. 42.
    D'Souza C, Kishore U, Tsolaki AG. 2023.. The PE-PPE family of Mycobacterium tuberculosis: proteins in disguise. . Immunobiology 228::152321
     [Crossref] [Google Scholar]
  43. 43.
    Fatima R, Usman M, Faryal R. 2020.. Association of TLR2 polymorphisms, Arg753Gln and Arg677Trp, with tuberculosis in Pakhtun population of Pakistan. . Infect. Genet. Evol. 83::104291
     [Crossref] [Google Scholar]
  44. 44.
    Fenner L, Egger M, Bodmer T, Furrer H, Ballif M, et al. 2013.. HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis. . PLOS Genet. 9::e1003318
     [Crossref] [Google Scholar]
  45. 45.
    Gagneux S. 2012.. Host-pathogen coevolution in human tuberculosis. . Philos. Trans. R. Soc. B 367::850–59
     [Crossref] [Google Scholar]
  46. 46.
    Harishankar M, Selvaraj P, Bethunaickan R. 2018.. Influence of genetic polymorphism towards pulmonary tuberculosis susceptibility. . Front. Med. 5::213
     [Crossref] [Google Scholar]
  47. 47.
    Harouna Hamidou Z, Morsli M, Mamadou S, Drancourt M, Saad J. 2022.. Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: a snapshot based on whole-genome sequencing. . PLOS Negl. Trop. Dis. 16::e0010443
     [Crossref] [Google Scholar]
  48. 48.
    Herb F, Thye T, Niemann S, Browne EN, Chinbuah MA, et al. 2008.. ALOX5 variants associated with susceptibility to human pulmonary tuberculosis. . Hum. Mol. Genet. 17::1052–60
     [Crossref] [Google Scholar]
  49. 49.
    Hershkovitz I, Donoghue HD, Minnikin DE, Besra GS, Lee OY, et al. 2008.. Detection and molecular characterization of 9,000-year-old Mycobacterium tuberculosis from a Neolithic settlement in the Eastern Mediterranean. . PLOS ONE 3::e3426
     [Crossref] [Google Scholar]
  50. 50.
    Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM. 2004.. Stable association between strains of Mycobacterium tuberculosis and their human host populations. . PNAS 101::4871–76
     [Crossref] [Google Scholar]
  51. 51.
    Hu L, Tao H, Tao X, Tang X, Xu C. 2019.. TLR2 Arg753Gln gene polymorphism associated with tuberculosis susceptibility: an updated meta-analysis. . Biomed. Res. Int. 2019::2628101
     [Google Scholar]
  52. 52.
    Intemann CD, Thye T, Niemann S, Browne EN, Amanua Chinbuah M, et al. 2009.. Autophagy gene variant IRGM −261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains. . PLOS Pathog. 5::e1000577
     [Crossref] [Google Scholar]
  53. 53.
    Ioana M, Ferwerda B, Plantinga TS, Stappers M, Oosting M, et al. 2012.. Different patterns of Toll-like receptor 2 polymorphisms in populations of various ethnic and geographic origins. . Infect. Immun. 80::1917–22
     [Crossref] [Google Scholar]
  54. 54.
    Jin HS, Cho JE, Park S. 2019.. Association between CD53 genetic polymorphisms and tuberculosis cases. . Genes Genom. 41::389–95
     [Crossref] [Google Scholar]
  55. 55.
    Jin X, Yin S, Zhang Y, Chen X. 2020.. Association between TLR2 Arg677Trp polymorphism and tuberculosis susceptibility: a meta-analysis. . Microb. Pathog. 144::104173
     [Crossref] [Google Scholar]
  56. 56.
    Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, et al. 1997.. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. . J. Clin. Microbiol. 35::907–14
     [Crossref] [Google Scholar]
  57. 57.
    Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, et al. 2015.. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. . Nat. Commun. 6::6717
     [Crossref] [Google Scholar]
  58. 58.
    Kerner G, Laval G, Patin E, Boisson-Dupuis S, Abel L, et al. 2021.. Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. . Am. J. Hum. Genet. 108::517–24
     [Crossref] [Google Scholar]
  59. 59.
    Kobayashi K, Yuliwulandari R, Yanai H, Lien LT, Hang NT, et al. 2011.. Association of CD209 polymorphisms with tuberculosis in an Indonesian population. . Hum. Immunol. 72::741–45
     [Crossref] [Google Scholar]
  60. 60.
    Kone A, Diarra B, Cohen K, Diabate S, Kone B, et al. 2019.. Differential HLA allele frequency in Mycobacterium africanum vs Mycobacterium tuberculosis in Mali. . HLA 93::24–31
     [Crossref] [Google Scholar]
  61. 61.
    Kozak RA, Alexander DC, Liao R, Sherman DR, Behr MA. 2011.. Region of difference 2 contributes to virulence of Mycobacterium tuberculosis. . Infect. Immun. 79::59–66
     [Crossref] [Google Scholar]
  62. 62.
    Lao W, Kang H, Jin G, Chen L, Chu Y, et al. 2017.. Evaluation of the relationship between MARCO and CD36 single-nucleotide polymorphisms and susceptibility to pulmonary tuberculosis in a Chinese Han population. . BMC Infect. Dis. 17::488
     [Crossref] [Google Scholar]
  63. 63.
    Le Hang NT, Hijikata M, Maeda S, Miyabayashi A, Wakabayashi K, et al. 2021.. Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam. . Sci. Rep. 11::13609
     [Crossref] [Google Scholar]
  64. 64.
    Leal D, Santana da Silva MN, Fernandes D, Rodrigues JCG, Barros M, et al. 2020.. Amerindian genetic ancestry as a risk factor for tuberculosis in an Amazonian population. . PLOS ONE 15::e0236033
     [Crossref] [Google Scholar]
  65. 65.
    Lee MR, Chen YL, Wu CW, Chen LC, Chang LY, et al. 2022.. Toll-like receptor and matrix metalloproteinase single-nucleotide polymorphisms, haplotypes, and polygenic risk score differentiated between tuberculosis disease and infection. . Int. J. Infect. Dis. 125::61–66
     [Crossref] [Google Scholar]
  66. 66.
    Li T, Wang L, Guo C, Zhang H, Xu P, et al. 2022.. Polymorphisms of SLC11A1(NRAMP1) rs17235409 associated with and susceptibility to spinal tuberculosis in a southern Han Chinese population. . Infect. Genet. Evol. 98::105202
     [Crossref] [Google Scholar]
  67. 67.
    Li X, Yang Y, Zhou F, Zhang Y, Lu H, et al. 2011.. SLC11A1 (NRAMP1) polymorphisms and tuberculosis susceptibility: updated systematic review and meta-analysis. . PLOS ONE 6::e15831
     [Crossref] [Google Scholar]
  68. 68.
    Liu CW, Lin CJ, Hu HC, Liu HJ, Chiu YC, et al. 2020.. The association of inflammasome and TLR2 gene polymorphisms with susceptibility to tuberculosis in the Han Taiwanese population. . Sci. Rep. 10::10184
     [Crossref] [Google Scholar]
  69. 69.
    Liu M, Wang Q, Liu H, Yin C, Mijiti X, et al. 2022.. Association of mannose-binding lectin 2 gene polymorphism with tuberculosis based on Mycobacterium tuberculosis lineages. . Infect. Drug Resist. 15::1225–34
     [Crossref] [Google Scholar]
  70. 70.
    Liu Q, Ma A, Wei L, Pang Y, Wu B, et al. 2018.. China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. . Nat. Ecol. Evol. 2::1982–92
     [Crossref] [Google Scholar]
  71. 71.
    Lopez MG, Campos-Herrero MI, Torres-Puente M, Canas F, Comin J, et al. 2023.. Deciphering the tangible spatio-temporal spread of a 25-year tuberculosis outbreak boosted by social determinants. . Microbiol. Spectr. 11::e0282622
     [Crossref] [Google Scholar]
  72. 72.
    Luo T, Comas I, Luo D, Lu B, Wu J, et al. 2015.. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. . PNAS 112::8136–41
     [Crossref] [Google Scholar]
  73. 73.
    Ma MJ, Wang HB, Li H, Yang JH, Yan Y, et al. 2011.. Genetic variants in MARCO are associated with the susceptibility to pulmonary tuberculosis in Chinese Han population. . PLOS ONE 6::e24069
     [Crossref] [Google Scholar]
  74. 74.
    Mazars E, Lesjean S, Banuls AL, Gilbert M, Vincent V, et al. 2001.. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. . PNAS 98::1901–6
     [Crossref] [Google Scholar]
  75. 75.
    McHenry ML, Bartlett J, Igo RP Jr., Wampande EM, Benchek P, et al. 2020.. Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution?. PLOS Genet. 16::e1008728
     [Crossref] [Google Scholar]
  76. 76.
    McHenry ML, Wampande EM, Joloba ML, Malone LL, Mayanja-Kizza H, et al. 2021.. Interaction between M. tuberculosis lineage and human genetic variants reveals novel pathway associations with severity of TB. . Pathogens 10::1487
     [Crossref] [Google Scholar]
  77. 77.
    McHenry ML, Williams SM, Stein CM. 2020.. Genetics and evolution of tuberculosis pathogenesis: new perspectives and approaches. . Infect. Genet. Evol. 81::104204
     [Crossref] [Google Scholar]
  78. 78.
    Medha, Sharma S, Sharma M. 2021.. Proline-Glutamate/Proline-Proline-Glutamate (PE/PPE) proteins of Mycobacterium tuberculosis: the multifaceted immune-modulators. . Acta Trop. 222::106035
     [Crossref] [Google Scholar]
  79. 79.
    Meilang Q, Zhang Y, Zhang J, Zhao Y, Tian C, et al. 2012.. Polymorphisms in the SLC11A1 gene and tuberculosis risk: a meta-analysis update. . Int. J. Tuberc. Lung Dis. 16::437–46
     [Crossref] [Google Scholar]
  80. 80.
    Menardo F, Rutaihwa LK, Zwyer M, Borrell S, Comas I, et al. 2021.. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. . F1000Research 10::60
     [Crossref] [Google Scholar]
  81. 81.
    Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, et al. 2015.. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. . Nat. Genet. 47::242–49
     [Crossref] [Google Scholar]
  82. 82.
    Miyahara R, Piboonsiri P, Chiyasirinroje B, Imsanguan W, Nedsuwan S, et al. 2023.. Risk for prison-to-community tuberculosis transmission, Thailand, 2017–2020. . Emerg. Infect. Dis. 29::477–83
     [Crossref] [Google Scholar]
  83. 83.
    Miyahara R, Smittipat N, Juthayothin T, Yanai H, Disratthakit A, et al. 2020.. Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country. . Tuberculosis 125::101991
     [Crossref] [Google Scholar]
  84. 84.
    Mokrousov I. 2013.. Insights into the origin, emergence, and current spread of a successful Russian clone of Mycobacterium tuberculosis. . Clin. Microbiol. Rev. 26::342–60
     [Crossref] [Google Scholar]
  85. 85.
    Mokrousov I. 2015.. Mycobacterium tuberculosis phylogeography in the context of human migration and pathogen's pathobiology: insights from Beijing and Ural families. . Tuberculosis 95:(Suppl. 1):S167–76
     [Crossref] [Google Scholar]
  86. 86.
    Möller M, Kinnear CJ. 2020.. Human global and population-specific genetic susceptibility to Mycobacterium tuberculosis infection and disease. . Curr. Opin. Pulm. Med. 26::302–10
     [Crossref] [Google Scholar]
  87. 87.
    Montalbetti N, Simonin A, Kovacs G, Hediger MA. 2013.. Mammalian iron transporters: families SLC11 and SLC40. . Mol. Aspects Med. 34::270–87
     [Crossref] [Google Scholar]
  88. 88.
    Muheremu A, Jiang J, Yakufu M, Aili A, Li L, Luo Z. 2022.. Relationship between tool-like receptor 4 gene polymorphism and the susceptibility to pulmonary tuberculosis. . Am. J. Transl. Res. 14::3893–903
     [Google Scholar]
  89. 89.
    Ndong Sima CAA, Smith D, Petersen DC, Schurz H, Uren C, Möller M. 2023.. The immunogenetics of tuberculosis (TB) susceptibility. . Immunogenetics 75::215–30
     [Crossref] [Google Scholar]
  90. 90.
    Ndzi EN, Nkenfou CN, Pefura EWY, Mekue LCM, Guiedem E, et al. 2019.. Tuberculosis diagnosis: algorithm that may discriminate latent from active tuberculosis. . Heliyon 5::e02559
     [Crossref] [Google Scholar]
  91. 91.
    Netikul T, Palittapongarnpim P, Thawornwattana Y, Plitphonganphim S. 2021.. Estimation of the global burden of Mycobacterium tuberculosis lineage 1. . Infect. Genet. Evol. 91::104802
     [Crossref] [Google Scholar]
  92. 92.
    Netikul T, Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, et al. 2022.. Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis lineage 1 in endemic regions of Asia and Africa. . Sci. Rep. 12::1565
     [Crossref] [Google Scholar]
  93. 93.
    Ogarkov O, Mokrousov I, Sinkov V, Zhdanova S, Antipina S, Savilov E. 2012.. “ Lethal” combination of Mycobacterium tuberculosis Beijing genotype and human CD209 −336G allele in Russian male population. . Infect. Genet. Evol. 12::732–36
     [Crossref] [Google Scholar]
  94. 94.
    Oliveira-Cortez A, Melo AC, Chaves VE, Condino-Neto A, Camargos P. 2016.. Do HLA class II genes protect against pulmonary tuberculosis? A systematic review and meta-analysis. . Eur. J. Clin. Microbiol. Infect. Dis. 35::1567–80
     [Crossref] [Google Scholar]
  95. 95.
    Omae Y, Toyo-Oka L, Yanai H, Nedsuwan S, Wattanapokayakit S, et al. 2017.. Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis. . J. Hum. Genet. 62::1015–22
     [Crossref] [Google Scholar]
  96. 96.
    O'Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, et al. 2019.. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. . Mol. Ecol. 28::3241–56
     [Crossref] [Google Scholar]
  97. 97.
    Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, et al. 2018.. Evidence for host-bacterial co-evolution via genome sequence analysis of 480 Thai Mycobacterium tuberculosis lineage 1 isolates. . Sci. Rep. 8::11597
     [Crossref] [Google Scholar]
  98. 98.
    Palittapongarnpim P, Luangsook P, Tansuphaswadikul S, Chuchottaworn C, Prachaktam R, Sathapatayavongs B. 1997.. Restriction fragment length polymorphism study of Mycobacterium tuberculosis in Thailand using IS6110 as probe. . Int. J. Tuberc. Lung Dis. 1::370–76
     [Google Scholar]
  99. 99.
    Perez-Lago L, Campos-Herrero MI, Canas F, Copado R, Sante L, et al. 2019.. A Mycobacterium tuberculosis Beijing strain persists at high rates and extends its geographic boundaries 20 years after importation. . Sci. Rep. 9::4687
     [Crossref] [Google Scholar]
  100. 100.
    Phelan JE, Gomez-Gonzalez PJ, Andreu N, Omae Y, Toyo-Oka L, et al. 2023.. Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. . Nat. Commun. 14::549
     [Crossref] [Google Scholar]
  101. 101.
    Phelan JE, Lim DR, Mitarai S, de Sessions PF, Tujan MAA, et al. 2019.. Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines. . Sci. Rep. 9::9305
     [Crossref] [Google Scholar]
  102. 102.
    Phyu AN, Aung ST, Palittapongarnpim P, Htet KKK, Mahasirimongkol S, et al. 2023.. Genomic sequencing profiles of Mycobacterium tuberculosis in Mandalay region, Myanmar. . Trop. Med. Infect. Dis. 8::239
     [Crossref] [Google Scholar]
  103. 103.
    Raberg L. 2023.. Human and pathogen genotype-by-genotype interactions in the light of coevolution theory. . PLOS Genet. 19::e1010685
     [Crossref] [Google Scholar]
  104. 104.
    Robinson J, Guethlein LA, Cereb N, Yang SY, Norman PJ, et al. 2017.. Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles. . PLOS Genet. 13::e1006862
     [Crossref] [Google Scholar]
  105. 105.
    Sabin S, Herbig A, Vagene AJ, Ahlstrom T, Bozovic G, et al. 2020.. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. . Genome Biol. 21::201
     [Crossref] [Google Scholar]
  106. 106.
    Sali M, Di Sante G, Cascioferro A, Zumbo A, Nicolo C, et al. 2010.. Surface expression of MPT64 as a fusion with the PE domain of PE_PGRS33 enhances Mycobacterium bovis BCG protective activity against Mycobacterium tuberculosis in mice. . Infect. Immun. 78::5202–13
     [Crossref] [Google Scholar]
  107. 107.
    Salie M, van der Merwe L, Möller M, Daya M, van der Spuy GD, et al. 2014.. Associations between human leukocyte antigen class I variants and the Mycobacterium tuberculosis subtypes causing disease. . J. Infect. Dis. 209::216–23
     [Crossref] [Google Scholar]
  108. 108.
    Sanchez-Mazas A. 2020.. A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations. . Swiss Med. Wkly. 150::w20214
     [Google Scholar]
  109. 109.
    Schurz H, Daya M, Möller M, Hoal EG, Salie M. 2015.. TLR1, 2, 4, 6 and 9 variants associated with tuberculosis susceptibility: a systematic review and meta-analysis. . PLOS ONE 10::e0139711
     [Crossref] [Google Scholar]
  110. 110.
    Shen C, Wu XR, Wang BB, Sun L, Jiao WW, et al. 2013.. ALOX5 is associated with tuberculosis in a subset of the pediatric population of North China. . Genet. Test Mol. Biomark. 17::284–88
     [Crossref] [Google Scholar]
  111. 111.
    Shitikov E, Bespiatykh D. 2023.. A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates. . mSphere 8::e0016923
     [Crossref] [Google Scholar]
  112. 112.
    Shitikov E, Kolchenko S, Mokrousov I, Bespyatykh J, Ischenko D, et al. 2017.. Evolutionary pathway analysis and unified classification of East Asian lineage of Mycobacterium tuberculosis. . Sci. Rep. 7::9227
     [Crossref] [Google Scholar]
  113. 113.
    Shuaib YA, Utpatel C, Kohl TA, Barilar I, Diricks M, et al. 2022.. Origin and global expansion of Mycobacterium tuberculosis complex lineage 3. . Genes 13::990
     [Crossref] [Google Scholar]
  114. 114.
    Simonds B. 1957.. Twin research in tuberculosis. . Eugen. Rev. 49::25–32
     [Google Scholar]
  115. 115.
    Singh UB, Suresh N, Bhanu NV, Arora J, Pant H, et al. 2004.. Predominant tuberculosis spoligotypes, Delhi, India. . Emerg. Infect. Dis. 10::1138–42
     [Crossref] [Google Scholar]
  116. 116.
    Smittipat N, Billamas P, Palittapongarnpim M, Thong-On A, Temu MM, et al. 2005.. Polymorphism of variable-number tandem repeats at multiple loci in Mycobacterium tuberculosis. . J. Clin. Microbiol. 43::5034–43
     [Crossref] [Google Scholar]
  117. 117.
    Smittipat N, Miyahara R, Juthayothin T, Billamas P, Dokladda K, et al. 2019.. Indo-Oceanic Mycobacterium tuberculosis strains from Thailand associated with higher mortality. . Int. J. Tuberc. Lung Dis. 23::972–79
     [Crossref] [Google Scholar]
  118. 118.
    Sola C, Filliol I, Legrand E, Mokrousov I, Rastogi N. 2001.. Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS1081, IS6110, VNTR, and DR-based spoligotyping suggests the existence of two new phylogeographical clades. . J. Mol. Evol. 53::680–89
     [Crossref] [Google Scholar]
  119. 119.
    Sousa AO, Salem JI, Lee FK, Vercosa MC, Cruaud P, et al. 1997.. An epidemic of tuberculosis with a high rate of tuberculin anergy among a population previously unexposed to tuberculosis, the Yanomami Indians of the Brazilian Amazon. . PNAS 94::13227–32
     [Crossref] [Google Scholar]
  120. 120.
    Srilohasin P, Chaiprasert A, Tokunaga K, Nishida N, Prammananan T, et al. 2014.. Genetic diversity and dynamic distribution of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in Thailand. . J. Clin. Microbiol. 52::4267–74
     [Crossref] [Google Scholar]
  121. 121.
    Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, et al. 2016.. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. . Nat. Genet. 48::1535–43
     [Crossref] [Google Scholar]
  122. 122.
    Swart Y, Uren C, van Helden PD, Hoal EG, Möller M. 2021.. Local ancestry adjusted allelic association analysis robustly captures tuberculosis susceptibility loci. . Front. Genet. 12::716558
     [Crossref] [Google Scholar]
  123. 123.
    Tantivitayakul P, Ruangchai W, Juthayothin T, Smittipat N, Disratthakit A, et al. 2020.. Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis. . Sci. Rep. 10::8024
     [Crossref] [Google Scholar]
  124. 124.
    Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Cui Z, et al. 2021.. Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2. . Microb. Genom. 7::000697
     [Google Scholar]
  125. 125.
    Thuong NT, Hawn TR, Chau TT, Bang ND, Yen NT, et al. 2012.. Epiregulin (EREG) variation is associated with susceptibility to tuberculosis. . Genes Immun. 13::275–81
     [Crossref] [Google Scholar]
  126. 126.
    Thuong NT, Tram TT, Dinh TD, Thai PV, Heemskerk D, et al. 2016.. MARCO variants are associated with phagocytosis, pulmonary tuberculosis susceptibility and Beijing lineage. . Genes Immun. 17::419–25
     [Crossref] [Google Scholar]
  127. 127.
    Thye T, Niemann S, Walter K, Homolka S, Intemann CD, et al. 2011.. Variant G57E of mannose binding lectin associated with protection against tuberculosis caused by Mycobacterium africanum but not by M. tuberculosis. . PLOS ONE 6::e20908
     [Crossref] [Google Scholar]
  128. 128.
    Tientcheu LD, Koch A, Ndengane M, Andoseh G, Kampmann B, Wilkinson RJ. 2017.. Immunological consequences of strain variation within the Mycobacterium tuberculosis complex. . Eur. J. Immunol. 47::432–45
     [Crossref] [Google Scholar]
  129. 129.
    Todros-Dawda I, Kveberg L, Vaage JT, Inngjerdingen M. 2014.. The tetraspanin CD53 modulates responses from activating NK cell receptors, promoting LFA-1 activation and dampening NK cell effector functions. . PLOS ONE 9::e97844
     [Crossref] [Google Scholar]
  130. 130.
    Tong X, Wan Q, Li Z, Liu S, Huang J, et al. 2019.. Association between the mannose-binding lectin (MBL)-2 gene variants and serum MBL with pulmonary tuberculosis: an update meta-analysis and systematic review. . Microb. Pathog. 132::374–80
     [Crossref] [Google Scholar]
  131. 131.
    Toyo-Oka L, Mahasirimongkol S, Yanai H, Mushiroda T, Wattanapokayakit S, et al. 2017.. Strain-based HLA association analysis identified HLA-DRB1*09:01 associated with modern strain tuberculosis. . HLA 90::149–56
     [Crossref] [Google Scholar]
  132. 132.
    van Crevel R, Parwati I, Sahiratmadja E, Marzuki S, Ottenhoff TH, et al. 2009.. Infection with Mycobacteriumtuberculosis Beijing genotype strains is associated with polymorphisms in SLC11A1/NRAMP1 in Indonesian patients with tuberculosis.. J. Infect. Dis. 200::1671–74
     [Crossref] [Google Scholar]
  133. 133.
    van der Eijk EA, van de Vosse E, Vandenbroucke JP, van Dissel JT. 2007.. Heredity versus environment in tuberculosis in twins: the 1950s United Kingdom Prophit survey—Simonds and Comstock revisited. . Am. J. Respir. Crit. Care Med. 176::1281–88
     [Crossref] [Google Scholar]
  134. 134.
    van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, et al. 1993.. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. . J. Clin. Microbiol. 31::406–9
     [Crossref] [Google Scholar]
  135. 135.
    van Embden JD, van Gorkom T, Kremer K, Jansen R, van der Zeijst BA, Schouls LM. 2000.. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. . J. Bacteriol. 182::2393–401
     [Crossref] [Google Scholar]
  136. 136.
    van Soolingen D, Qian L, de Haas PE, Douglas JT, Traore H, et al. 1995.. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia. . J. Clin. Microbiol. 33::3234–38
     [Crossref] [Google Scholar]
  137. 137.
    Van Valen L. 1974.. Molecular evolution as predicted by natural selection. . J. Mol. Evol. 3::89–101
     [Crossref] [Google Scholar]
  138. 138.
    Wang L, Chen RF, Liu JW, Lee IK, Lee CP, et al. 2011.. DC-SIGN (CD209) promoter −336 A/G polymorphism is associated with dengue hemorrhagic fever and correlated to DC-SIGN expression and immune augmentation. . PLOS Negl. Trop. Dis. 5::e934
     [Crossref] [Google Scholar]
  139. 139.
    White MJ, Tacconelli A, Chen JS, Wejse C, Hill PC, et al. 2014.. Epiregulin (EREG) and human V-ATPase (TCIRG1): genetic variation, ethnicity and pulmonary tuberculosis susceptibility in Guinea-Bissau and The Gambia. . Genes Immun. 15::370–77
     [Crossref] [Google Scholar]
  140. 140.
    Wirth T, Hildebrand F, Allix-Beguec C, Wolbeling F, Kubica T, et al. 2008.. Origin, spread and demography of the Mycobacterium tuberculosis complex. . PLOS Pathog. 4::e1000160
     [Crossref] [Google Scholar]
  141. 141.
    Xie H, Li C, Zhang M, Zhong N, Chen L. 2017.. Association between IRGM polymorphisms and tuberculosis risk: a meta-analysis. . Medicine 96::e8189
     [Crossref] [Google Scholar]
  142. 142.
    Yi L, Zhang K, Mo Y, Zhen G, Zhao J. 2015.. The association between CD209 gene polymorphisms and pulmonary tuberculosis susceptibility: a meta-analysis. . Int. J. Clin. Exp. Pathol. 8::12437–45
     [Google Scholar]
  143. 143.
    Yim JJ, Selvaraj P. 2010.. Genetic susceptibility in tuberculosis. . Respirology 15::241–56
     [Crossref] [Google Scholar]
  144. 144.
    Zafar A, Shafiq M, Ali B, Sadee W, Shakoori AR, Shakoori FR. 2022.. Association of IRGM promoter region polymorphisms and haplotype with pulmonary tuberculosis in Pakistani (Punjab) population. . Tuberculosis 136::102233
     [Crossref] [Google Scholar]
  145. 145.
    Zein-Eddine R, Refregier G, Cervantes J, Yokobori NK. 2023.. The future of CRISPR in Mycobacterium tuberculosis infection. . J. Biomed. Sci. 30::34
     [Crossref] [Google Scholar]
  146. 146.
    Zhang FR, Huang W, Chen SM, Sun LD, Liu H, et al. 2009.. Genomewide association study of leprosy. . N. Engl. J. Med. 361::2609–18
     [Crossref] [Google Scholar]
  147. 147.
    Zhang J, Wang MG, He JQ. 2023.. Association between a single nucleotide polymorphism of the ALOX5 gene and susceptibility to multisystem tuberculosis in a Chinese Han population. . Microb. Pathog. 183::106289
     [Crossref] [Google Scholar]
  148. 148.
    Zhang J, Zhao Z, Zhong H, Wu L, Zhou W, et al. 2018.. Importance of common TLR2 genetic variants on clinical phenotypes and risk in tuberculosis disease in a Western Chinese population. . Infect. Genet. Evol. 60::173–80
     [Crossref] [Google Scholar]
  149. 149.
    Zhang JX, Gong WP, Zhu DL, An HR, Yang YR, et al. 2020.. Mannose-binding lectin 2 gene polymorphisms and their association with tuberculosis in a Chinese population. . Infect. Dis. Poverty 9::46
     [Crossref] [Google Scholar]
  150. 150.
    Zhang L, Pang Y, Yu X, Wang Y, Lu J, et al. 2016.. Risk factors for pulmonary cavitation in tuberculosis patients from China. . Emerg. Microbes Infect. 5::e110
     [Google Scholar]
  151. 151.
    Zhou Y, Zhang M. 2020.. Associations between genetic polymorphisms of TLRs and susceptibility to tuberculosis: a meta-analysis. . Innate Immun. 26::75–83
     [Crossref] [Google Scholar]
  152. 152.
    Zhou Z, Yi H, Zhou Q, Wang L, Zhu Y, et al. 2023.. Evolution and epidemic success of Mycobacterium tuberculosis in eastern China: evidence from a prospective study. . BMC Genom. 24::241
     [Crossref] [Google Scholar]
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Genomic Interactions Between Mycobacterium tuberculosis and Humans
Annual Review of Genomics and Human Genetics 25, 183 (2024); https://doi.org/10.1146/annurev-genom-021623-101844
/content/journals/10.1146/annurev-genom-021623-101844
/content/journals/10.1146/annurev-genom-021623-101844
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