Co-evolution of Mycobacterium tuberculosis and Homo sapiens

Immunological Reviews

Volumn 264, Issue 1, 2015, Pages 6-24

  Brites, Daniela ^a   Gagneux, Sebastien ^a  

^a SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

Author keywords

Adaptation; Host; Pathogen; Selection; Virulence

Indexed keywords

BCG VACCINE;

ARTICLE; BACTERIAL VIRULENCE; COEVOLUTION; DEMOGRAPHY; DISEASE ASSOCIATION; DNA SEQUENCE; EVOLUTIONARY ADAPTATION; GENETIC DRIFT; GENETIC POLYMORPHISM; GENOTYPE; HOST PATHOGEN INTERACTION; HUMAN; LOCAL ADAPTATION; MOLECULAR INTERACTION; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS COMPLEX; PRIORITY JOURNAL; TUBERCULOSIS; ADAPTATION; ANIMAL; BACTERIAL GENOME; CLASSIFICATION; DISEASE PREDISPOSITION; EVOLUTION; GENETICS; IMMUNOLOGY; MICROBIOLOGY; PATHOGENICITY; PHYLOGENY; PHYSIOLOGY; TIME; VIRULENCE;

ADAPTATION, BIOLOGICAL; ANIMALS; BIOLOGICAL EVOLUTION; DISEASE SUSCEPTIBILITY; GENETIC DRIFT; GENOME, BACTERIAL; HOST-PATHOGEN INTERACTIONS; HUMANS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; TIME FACTORS; TUBERCULOSIS; VIRULENCE;

EID: 84923171582     PISSN: 01052896     EISSN: 1600065X     Source Type: Journal    
DOI: 10.1111/imr.12264     Document Type: Article

References (161)

1. Buckling A, Rainey PB. Antagonistic coevolution between a bacterium and a bacteriophage. Proc R Soc Lond B Biol Sci 2002;269:931-936.
2. Betts A, Kaltz O, Hochberg ME. Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages. Proc Natl Acad Sci USA 2014;111:11109-11114.
3. Sorci G, Moller AP, Boulinier T. Genetics of host-parasite interactions. Trends Ecol Evol 1997;12:196-200.
4. Karlsson EK, Kwiatkowski DP, Sabeti PC. Natural selection and infectious disease in human populations. Nat Rev Genet 2014;15:379-393.
5. Anderson RM, May RM. Coevolution of hosts and parasites. Parasitology 1982;85(Pt 2):411-426.
6. May RM, Anderson RM. Epidemiology and genetics in the coevolution of parasites and hosts. Proc R Soc Lond B Biol Sci 1983;219:281-313.
7. Woolhouse ME, Webster JP, Domingo E, Charlesworth B, Levin BR. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat Genet 2002;32:569-577.
8. Hamilton WD. Sex versus non-sex versus parasite. Oikos 1980;35:282-290.
9. WHO. Global Tuberculosis Report 2013. Geneva, Switzerland: World Health Organization, 2013.
10. Copin R, Coscolla M, Efstathiadis E, Gagneux S, Ernst JD. Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG). Vaccine 2014;32:5998-6004.
11. O'Garra A, Redford PS, McNab FW, Bloom CI, Wilkinson RJ, Berry MP. The immune response in tuberculosis. Annu Rev Immunol 2013;31:475-527.
12. Ernst JD. The immunological life cycle of tuberculosis. Nat Rev Immunol 2012;12:581-591.
13. Esmail H, Barry CE 3rd, Young DB, Wilkinson RJ. The ongoing challenge of latent tuberculosis. Philos Trans R Soc Lond B Biol Sci 2014;369:20130437.
14. Young DB, Gideon HP, Wilkinson RJ. Eliminating latent tuberculosis. Trends Microbiol 2009;17:183-188.
15. Coscolla M, Gagneux S. Does M. tuberculosis genomic diversity explain disease diversity? Drug Discov Today 2010;7:e43-e59.
16. Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014;26:441-444.
17. Comas I, Gagneux S. The past and future of tuberculosis research. PLoS Pathog 2009;5:e1000600.
18. Young D, Verreck FA. Creativity in tuberculosis research and discovery. Tuberculosis 2012;92(Suppl 1):S14-S16.
19. Smith NH, et al. Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol 2006;239:220-225.
20. Brosch R, et al. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 2002;99:3684-3689.
21. Mostowy S, Cousins D, Brinkman J, Aranaz A, Behr MA. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis 2002;186:74-80.
22. Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson G. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nature Rev Microbiol 2006;4:670-681.
23. Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM. Stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc Natl Acad Sci USA 2004;101:4871-4876.
24. Gagneux S, et al. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2006;103:2869-2873.
25. Tsolaki AG, et al. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci USA 2004;101:4865-4870.
26. Hershberg R, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2008;6:e311.
27. Comas I, et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 2010;42:498-503.
28. Firdessa R, et al. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis 2013;19:460-463.
29. Comas I, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 2013;45:1176-1182.
30. de Jong BC, Antonio M, Gagneux S. Mycobacterium africanum-review of an important cause of human tuberculosis in West Africa. PLoS Negl Trop Dis 2010;4:e744.
31. Coscolla M, et al. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis 2013;19:969-976.
32. Wirth T, et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog 2008;4:e1000160.
33. KoroKoro F, et al. Population dynamics of tuberculous Bacilli in Cameroon as assessed by spoligotyping. J Clin Microbiol 2012;51:299-302.
34. Wampande EM, et al. Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease. BMC Infect Dis 2013;13:484.
35. Paulsen HJ. Tuberculosis in the native American: indigenous or introduced? Rev Infect Dis 1987;9:1180-1186.
36. Kirzinger MW, Stavrinides J. Host specificity determinants as a genetic continuum. Trends Microbiol 2012;20:88-93.
37. Rivero A, et al. High rate of tuberculosis reinfection during a nosocomial outbreak of multidrug-resistant tuberculosis caused by Mycobacterium bovis strain B. Clin Infect Dis 2001;32:159-161.
38. Ameni G, et al. Mycobacterium tuberculosis infection in grazing cattle in central Ethiopia. Vet J 2011;188:359-361.
39. Taylor GM, Murphy E, Hopkins R, Rutland P, Chistov Y. First report of Mycobacterium bovis DNA in human remains from the Iron Age. Microbiology 2007;153:1243-1249.
40. Bos KI, et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 2014;514:494-497.
41. Mackowiak PA, Blos VT, Aguilar M, Buikstra JE. On the origin of American tuberculosis. Clin Infect Dis 2005;41:515-518.
42. Berg S, Smith NH. Why doesn't bovine tuberculosis transmit between humans? Trends Microbiol 2014;22:552-553.
43. Smith NH, Crawshaw T, Parry J, Birtles RJ. Mycobacterium microti: more diverse than previously thought. J Clin Microbiol 2009;47:2551-2559.
44. Wagner JC, Buchanan G, Bokkenheuser V, Leviseur S. An acid-fast bacillus isolated from the lungs of the Cape hyrax, Procavia capensis (Pallas). Nature 1958;181:284-285.
45. Mostowy S, Cousins D, Behr MA. Genomic interrogation of the dassie bacillus reveals it as a unique RD1 mutant within the Mycobacterium tuberculosis complex. J Bacteriol 2004;186:104-109.
46. Schoepf K, et al. A two-years' survey on the prevalence of tuberculosis caused by Mycobacterium caprae in red deer (Cervus elaphus) in the Tyrol, Austria. ISRN Vet Sci 2012;2012:245138.
47. Chiari M, et al. Isolation of Mycobacterium caprae (Lechtal genotype) from red deer (Cervus elaphus) in Italy. J Wildl Dis 2014;50:330-333.
48. Jenkins HE, Cox DR, Delahay RJ. Direction of association between bite wounds and Mycobacterium bovis infection in badgers: implications for transmission. PLoS ONE 2012;7:e45584.
49. van Ingen J, et al. Characterization of Mycobacterium orygis as M. tuberculosis complex subspecies. Emerg Infect Dis 2012;18:653-655.
50. Gey van Pittius NC, van Helden PD, Warren RM. Characterization of Mycobacterium orygis. Emerg Infect Dis 2012;18:1708-1709.
51. Alexander KA, et al. Novel Mycobacterium tuberculosis complex pathogen, M. mungi. Emerg Infect Dis 2010;16:1296-1299.
52. Parsons DC, Drewe JA, Gey van Pittius NC, Warren RM, van Helden PD. Novel cause of tuberculosis in Meerkats. South Africa. Emerg Infect Dis 2013;19:2004-2007.
53. Gutierrez MC, et al. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog 2005;1:e5.
54. Gonzalo-Asensio J, et al. Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator. Proc Natl Acad Sci USA 2014;111:11491-11496.
55. Walters SB, Dubnau E, Kolesnikova I, Laval F, Daffe M, Smith I. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol Microbiol 2006;60:312-330.
56. van Soolingen D, et al. A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int J Syst Bacteriol 1997;47:1236-1245.
57. Supply P, et al. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet 2013;45:172-179.
58. Veyrier FJ, Dufort A, Behr MA. The rise and fall of the Mycobacterium tuberculosis genome. Trends Microbiol 2011;19:156-161.
59. Jang J, Becq J, Gicquel B, Deschavanne P, Neyrolles O. Horizontally acquired genomic islands in the tubercle bacilli. Trends Microbiol 2008;16:303-308.
60. Namouchi A, Didelot X, Schock U, Gicquel B, Rocha EP. After the bottleneck: genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 2012;22:721-734.
61. Blouin Y, et al. Progenitor "Mycobacterium canettii" clone responsible for lymph node tuberculosis epidemic, Djibouti. Emerg Infect Dis 2014;20:21-28.
62. Koeck JL, et al. Clinical characteristics of the smooth tubercle bacilli 'Mycobacterium canettii' infection suggest the existence of an environmental reservoir. Clin Microbiol Infect 2010;17:1013-1019.
63. Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B, Neyrolles O. Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis. Mol Biol Evol 2006;23:1129-1135.
64. Cole ST, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393:537-544.
65. Uplekar S, Heym B, Friocourt V, Rougemont J, Cole ST. Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation. Infect Immun 2011;79:4042-4049.
66. Ramaswamy V, et al. Listeria-review of epidemiology and pathogenesis. J Microbiol Immunol Infect 2007;40:4-13.
67. Salinas C, et al. [Longitudinal incidence of tuberculosis in a cohort of contacts: factors associated with the disease]. Arch Bronconeumol 2007;43:317-323.
68. Rodrigo T, et al. Characteristics of tuberculosis patients who generate secondary cases. Int J Tuberc Lung Dis 1997;1:352-357.
69. Rouillon A, Perdrizet S, Parrot R. Transmission of tubercle bacilli: the effects of chemotherapy. Tubercle 1976;57:275-299.
70. Rose CE Jr, Zerbe GO, Lantz SO, Bailey WC. Establishing priority during investigation of tuberculosis contacts. Am Rev Respir Dis 1979;119:603-609.
71. Capewell S, Leitch AG. The value of contact procedures for tuberculosis in Edinburgh. Br J Dis Chest 1984;78:317-329.
72. Clark M, Riben P, Nowgesic E. The association of housing density, isolation and tuberculosis in Canadian First Nations communities. Int J Epidemiol 2002;31:940-945.
73. Anderson RM, May RM. Population biology of infectious diseases: part I. Nature 1979;280:361-367.
74. Levin BR. The evolution and maintenance of virulence in microparasites. Emerg Infect Dis 1996;2:93-102.
75. Kawecki TJ, Ebert D. Conceptual issues in local adaptation. Ecol Lett 2004;7:1225-1241.
76. Blanquart F, Kaltz O, Nuismer SL, Gandon S. A practical guide to measuring local adaptation. Ecol Lett 2013;16:1195-1205.
77. Gandon S, Van Zandt PA. Local adaptation and host-parasite interactions. Trends Ecol Evol 1998;13:214-216.
78. Reed MB, et al. Major Mycobacterium tuberculosis lineages associate with patient country of origin. J Clin Microbiol 2009;47:1119-1128.
79. Baker L, Brown T, Maiden MC, Drobniewski F. Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg Infect Dis 2004;10:1568-1577.
80. Fenner L, et al. HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis. PLoS Genet 2013;9:e1003318.
81. Pasipanodya JG, et al. Allopatric tuberculosis host-pathogen relationships are associated with greater pulmonary impairment. Infect Genet Evol 2013;16:433-440.
82. Groenheit R, et al. The Guinea-Bissau family of Mycobacterium tuberculosis complex revisited. PLoS ONE 2011;6:e18601.
83. Niobe-Eyangoh SN, et al. Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J Clin Microbiol 2003;41:2547-2553.
84. Godreuil S, et al. First molecular epidemiology study of Mycobacterium tuberculosis in Burkina Faso. J Clin Microbiol 2007;45:921-927.
85. de Jong BC, et al. Differences between tuberculosis cases infected with Mycobacterium africanum, West African type 2, relative to Euro-American Mycobacterium tuberculosis: an update. FEMS Immunol Med Microbiol 2010;58:102-105.
86. Bold TD, Davis DC, Penberthy KK, Cox LM, Ernst JD, de Jong BC. Impaired fitness of Mycobacterium africanum despite secretion of ESAT-6. J Infect Dis 2012;205:984-990.
87. de Jong BC, et al. Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts. J Infect Dis 2006;193:1279-1286.
88. Pai M, Zwerling A, Menzies D. Systematic review: T-cell-based assays for the diagnosis of latent tuberculosis infection: an update. Ann Intern Med 2008;149:177-184.
89. Blaser MJ, Kirschner D. The equilibria that allow bacterial persistence in human hosts. Nature 2007;449:843-849.
90. Gengenbacher M, Kaufmann SH. Mycobacterium tuberculosis: success through dormancy. FEMS Microbiol Rev 2012;36:514-532.
91. Ehrt S, Rhee K. Mycobacterium tuberculosis metabolism and host interaction: mysteries and paradoxes. Curr Top Microbiol Immunol 2012;374:163-188.
92. Zheng N, Whalen CC, Handel A. Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency. PLoS ONE 2014;9:e105721.
93. de Jong BC, et al. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J Infect Dis 2008;198:1037-1043.
94. Moller M, Hoal EG. Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis. Tuberculosis 2010;90:71-83.
95. Abel L, El-Baghdadi J, Bousfiha AA, Casanova JL, Schurr E. Human genetics of tuberculosis: a long and winding road. Philos Trans R Soc Lond B Biol Sci 2014;369:20130428.
96. Stead WW, Senner JW, Reddick WT, Lofgren JP. Racial differences in susceptibility to infection by Mycobacterium tuberculosis. N Engl J Med 1990;322:422-427.
97. Stead WW. Genetics and resistance to tuberculosis. Could resistance be enhanced by genetic engineering? Ann Intern Med 1992;116:937-941.
98. Li HT, Zhang TT, Zhou YQ, Huang QH, Huang J. SLC11A1 (formerly NRAMP1) gene polymorphisms and tuberculosis susceptibility: a meta-analysis. Int J Tuberc Lung Dis 2006;10:3-12.
99. Greenwood CM, et al. Linkage of tuberculosis to chromosome 2q35 loci, including NRAMP1, in a large aboriginal Canadian family. Am J Hum Genet 2000;67:405-416.
100. Malik S, et al. Alleles of the NRAMP1 gene are risk factors for pediatric tuberculosis disease. Proc Natl Acad Sci USA 2005;102:12183-12188.
101. Young D, Perkins MD, Duncan K, Barry CE 3rd. Confronting the scientific obstacles to global control of Tuberculosis. J Clin Invest 2008;118:1255-1265.
102. Caws M, et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog 2008;4:e1000034.
103. Thye T, et al. Variant G57E of mannose binding lectin associated with protection against tuberculosis caused by Mycobacterium africanum but not by M. tuberculosis. PLoS ONE 2011;6:e20908.
104. Intemann CD, et al. Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains. PLoS Pathog 2009;5:e1000577.
105. Salie M, et al. Associations between human leukocyte antigen class I variants and the Mycobacterium tuberculosis subtypes causing disease. J Infect Dis 2014;209:216-223.
106. Bartha I, et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. Elife 2013;2:e01123.
107. Pepperell CS, et al. The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog 2013;9:e1003543.
108. Hughes AL, Friedman R, Murray M. Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis. Emerg Infect Dis 2002;8:1342-1346.
109. Morelli G, et al. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet 2010;6:e1001036.
110. Kuo CH, Ochman H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol Direct 2009;4:35.
111. 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 2009;4:e7815.
112. Ford CB, et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet 2011;43:482-486.
113. Walker TM, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013;13:137-146.
114. Moran NA, Munson MA, Baumann P, Ishikawa H. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc Lond B Biol Sci 1993;253:167-171.
115. Moodley Y, et al. The peopling of the Pacific from a bacterial perspective. Science 2009;323:527-530.
116. Jin L, Su B. Natives or immigrants: modern human origin in east Asia. Nat Rev Genet 2000;1:126-133.
117. Stewart JR, Stringer CB. Human evolution out of Africa: the role of refugia and climate change. Science 2012;335:1317-1321.
118. Charleston MA, Robertson DL. Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Syst Biol 2002;51:528-535.
119. Paterson AM, Banks J. Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly. Int J Parasitol 2001;31:1012-1022.
120. Underhill PA, Kivisild T. Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 2007;41:539-564.
121. 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;10:103-111.
122. Pepperell CS, et al. Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc Natl Acad Sci USA 2011;108:6526-6531.
123. Kim TH, Kubica GP. Long-term preservation and storage of mycobacteria. Appl Microbiol 1972;24:311-317.
124. Bryant JM, et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med 2013;1:786-792.
125. Bryant JM, et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 2013;13:110.
126. Chan JZ, et al. Metagenomic analysis of tuberculosis in a mummy. N Engl J Med 2013;369:289-290.
127. Ho SY, Shapiro B, Phillips MJ, Cooper A, Drummond AJ. Evidence for time dependency of molecular rate estimates. Syst Biol 2007;56:515-522.
128. Rocha EP, et al. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol 2006;239:226-235.
129. KNOWLEDGE IFTSOH. Available at: http://www.humanjourney.us.
130. Foundation S. Available at: http://www.silkroadfoundation.org/toc/index.html.
131. Donoghue HD, et al. Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA. Lancet Infect Dis 2004;4:584-592.
132. Djelouadji Z, Raoult D, Drancourt M. Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome. Lancet Infect Dis 2011;11:641-650.
133. Rothschild BM, et al. Mycobacterium tuberculosis complex DNA from an extinct bison dated 17, 000 years before the present. Clin Infect Dis 2001;33:305-311.
134. Thierry D, et al. IS6110, an IS-like element of Mycobacterium tuberculosis complex. Nucleic Acids Res 1990;18:188.
135. Coros A, DeConno E, Derbyshire KM. IS6110, a Mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of Mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species. J Bacteriol 2008;190:3408-3410.
136. He L, Fan X, Xie J. Comparative genomic structures of Mycobacterium CRISPR-Cas. J Cell Biochem 2012;113:2464-2473.
137. Hershkovitz I, et al. Detection and molecular characterization of 9, 000-year-old Mycobacterium tuberculosis from a Neolithic settlement in the Eastern Mediterranean. PLoS ONE 2008;3:e3426.
138. Donoghue HD, et al. Biomolecular archaeology of ancient tuberculosis: response to "Deficiencies and challenges in the study of ancient tuberculosis DNA" by Wilbur et al. (2009). J Archaeol Sci 2009;36:2797-2804.
139. Wilbur AK, et al. Deficiencies and challenges in the study of ancient tuberculosis DNA. J Archaeol Sci 2009;36:1990-1997.
140. Nicklisch N, et al. Rib lesions in skeletons from early neolithic sites in Central Germany: on the trail of tuberculosis at the onset of agriculture. Am J Phys Anthropol 2012;149:391-404.
141. Zink AR, et al. Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J Clin Microbiol 2003;41:359-367.
142. Taylor GM, Young DB, Mays SA. Genotypic analysis of the earliest known prehistoric case of tuberculosis in Britain. J Clin Microbiol 2005;43:2236-2240.
143. Muller R, Roberts CA, Brown TA. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity. Proc R Soc Lond B Biol Sci 2014;281:20133236.
144. Kwan CK, Ernst JD. HIV and tuberculosis: a deadly human syndemic. Clin Microbiol Rev 2011;24:351-376.
145. Huang CC, et al. The effect of HIV-related immunosuppression on the risk of tuberculosis transmission to household contacts. Clin Infect Dis 2014;58:765-774.
146. Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004;38:615-643.
147. Deitsch KW, Lukehart SA, Stringer JR. Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens. Nat Rev Microbiol 2009;7:493-503.
148. Brennan MJ, Delogu G. The PE multigene family: a 'molecular mantra' for mycobacteria. Trends Microbiol 2002;10:246-249.
149. McEvoy CR, et al. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS ONE 2012;7:e30593.
150. Copin R, et al. Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. MBio 2014;5:e00960-00913.
151. Arjan JA, Visser M, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE. Diminishing returns from mutation supply rate in asexual populations. Science 1999;283:404-406.
152. Rice WR. Experimental tests of the adaptive significance of sexual recombination. Nat Rev Genet 2002;3:241-251.
153. Osorio NS, et al. Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure. Mol Biol Evol 2013;30:1326-1336.
154. Achtman M. Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2012;367:860-867.
155. Lipsitch M, Sousa AO. Historical intensity of natural selection for resistance to tuberculosis. Genetics 2002;161:1599-1607.
156. Barnes I, Duda A, Pybus OG, Thomas MG. Ancient urbanization predicts genetic resistance to tuberculosis. Evolution 2010;65:842-848.
157. Williams A, Dunbar RIM. Big brains, meat, tuberculosis and the nicotinamide switches: co-evolutionary relationships with modern repercussions on longevity and disease? Int J Tryptophan Res 2013;15:73-88.
158. Brites D, Gagneux S. Old and new selective pressures on Mycobacterium tuberculosis. Infect Genet Evol 2012;12:678-685.
159. Rose G, Cortes T, Comas I, Coscolla M, Gagneux S, Young DB. Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome Biol Evol 2013;5:1849-1862.
160. Lin PL, et al. Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing. Nat Med 2014;20:75-79.
161. Kodaman N, Sobota RS, Mera R, Schneider BG, Williams SM. Disrupted human-pathogen co-evolution: a model for disease. Front Genet 2014;5:290.