Genotype of a historic strain of Mycobacterium tuberculosis

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 45, 2012, Pages 18511-18516

  Bouwman, Abigail S ^a,d   Kennedy, Sandra L ^a   Mul̈ler, Romy ^a   Stephens, Richard H ^a   Holst, Malin ^b   Caffell, Anwen C ^c   Roberts, Charlotte A ^c   Brown, Terence A ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b YORK OSTEOARCHAEOLOGY LTD   (United Kingdom)

^c DURHAM UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Biomolecular archaeology; Paleopathology

Indexed keywords

ADOLESCENT; ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DNA HYBRIDIZATION; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENOTYPE; HUMAN; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; ENGLAND; FEMALE; GENOME, BACTERIAL; GENOTYPE; HUMANS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; OLIGONUCLEOTIDES; PALEONTOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

MYCOBACTERIUM TUBERCULOSIS;

EID: 84868519234     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1209444109     Document Type: Article

References (64)

1. Morse D (1967) Tuberculosis. Diseases in Antiquity, eds Brothwell D, Sandison AT (Charles Thomas, Springfield, IL), pp 249-271.
2. Canci A, Minozzi S, Tarli S (1996) New evidence of tuberculous spodylitis from Neolithic Liguria (Italy). Int J Osteoarchaeol 6(5):497-501. (Pubitemid 126434694)
3. Wilbur AK, et al. (2009) Deficiencies and challenges in the study of ancient tuberculosis. J Archaeol Sci 36(9):1990-1997.
4. Roberts CA, Pfister L-A, Mays S (2009) Letter to the editor: Was tuberculosis present in Homo erectus in Turkey? Am J Phys Anthropol 139(3):442-444.
5. Brosch R, et al. (2002) A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 99(6):3684-3689. (Pubitemid 34252166)
6. Baker L, Brown T, Maiden MC, Drobniewski F (2004) Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis. Emerg Infect Dis 10(9):1568-1577. (Pubitemid 39201508)
7. Mostowy S, Behr MA (2005) The origin and evolution of Mycobacterium tuberculosis. Clin Chest Med 26(2):207-216.
8. Gagneux S, et al. (2006) Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103(8):2869-2873.
9. Gagneux S, Small PM (2007) Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis 7(5):328-337. (Pubitemid 46590063)
10. Smith NH, Hewinson RG, Kremer K, Brosch R, Gordon SV (2009) Myths and misconceptions: The origin and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol 7(7):537-544.
11. Roberts CA, Buikstra JE (2008) The Bioarchaeology of Tuberculosis: A Global View on a Reemerging Disease (University Press of Florida, Gainesville, FL).
12. Ott K (1996) Fevered Lives: Tuberculosis in American Culture Since 1870 (Harvard Univ Press, Cambridge MA).
13. Dubos RJ, Dubos J (1952) The White Plague: Tuberculosis, Man, and Society (Rutgers Univ Press, Piscataway, NJ).
14. Clarkson L (1975) Death, Disease and Famine in Preindustrial England (Gill and Macmillan, Dublin).
15. Roberts CA, Cox M (2003) Health and Disease in Britain: From Prehistory to the Present Day (Sutton Publishing, Stroud, Gloucestershire, UK).
16. Lönnroth K, Jaramillo E, Williams BG, Dye C, Raviglione M (2009) Drivers of tuberculosis epidemics: The role of risk factors and social determinants. Soc Sci Med 68(12):2240-2246.
17. Smith ER (1988) The Retreat of Tuberculosis 1850-1950 (Croom Helm, London).
18. Anon (1993) WHO declares tuberculosis a global emergency. Soz Praventivmed 38(4):251-252.
19. World Health Organization (2011) Global Tuberculosis Control. WHO Report 2011 (WHO Press, Geneva).
20. Comas I, Homolka S, Niemann S, Gagneux S (2009) Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One 4(11):e7815.
21. Achtman M (2008) Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 62:53-70.
22. Hershberg R, et al. (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 6(12):e311.
23. Tanaka MM, Francis AR (2006) Detecting emerging strains of tuberculosis by using spoligotypes. Proc Natl Acad Sci USA 103(41):15266-15271. (Pubitemid 44583199)
24. Atkins P (2000) Milk consumption and tuberculosis in Britain 1850-1950. Order and Disorder: The Health Implications of Eating and Drinking in the 19th and 20th Centuries, ed Fenton A (Tuckwell, Edinburgh), pp 83-95.
25. Pfeiffer DU (2008) Animal tuberculosis. Clinical Tuberculosis, eds Davies PDO, Barnes PF, Gordon SB (Hodder Arnold, London), 4th Ed, pp 519-528.
26. Jaffe HL (1972) Metabolic, Degenerative and Inflammatory Diseases of Bones and Joints (Lea and Febiger, Philadelphia).
27. Roberts CA (2012) Re-emerging infections: Developments in bioarchaeological contributions to understanding tuberculosis today. A Companion to Palaeopathology, ed Grauer A (Blackwell, Oxford), pp 434-457.
28. Brown TA, Brown KA (2011) Biomolecular Archaeology: An Introduction (Wiley-Blackwell, Malden, MA).
29. Willerslev E, Cooper A (2005) Ancient DNA. Proc Biol Sci 272(1558):3-16.
30. Salo WL, Aufderheide AC, Buikstra J, Holcomb TA (1994) Identification of Mycobacterium tuberculosis DNA in a pre-Columbian Peruvian mummy. Proc Natl Acad Sci USA 91(6):2091-2094. (Pubitemid 24092048)
31. Taylor GM, Goyal M, Legge AJ, Shaw RJ, Young D (1999) Genotypic analysis of Mycobacterium tuberculosis from medieval human remains. Microbiology 145(Pt 4):899-904. (Pubitemid 29179206)
32. Taylor GM, Young DB, Mays SA (2005) Genotypic analysis of the earliest known prehistoric case of tuberculosis in Britain. J Clin Microbiol 43(5):2236-2240. (Pubitemid 40656233)
33. Taylor GM, Murphy E, Hopkins R, Rutland P, Chistov Y (2007) First report of Mycobacterium bovis DNA in human remains from the Iron Age. Microbiology 153(Pt 4):1243-1249. (Pubitemid 46605822)
34. Collins DM, Stephens DM (1991) Identification of insertion sequence, IS1081, in Mycobacterium bovis . FEMS Microbiol Lett 67(1):11-16.
35. Thierry D, et al. (1990) Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis. J Clin Microbiol 28(12):2668-2673.
36. Fletcher HA, Donoghue HD, Taylor GM, van der Zanden AG, Spigelman M (2003) Molecular analysis of Mycobacterium tuberculosis DNA from a family of 18th century Hungarians. Microbiology 149(Pt 1):143-151. (Pubitemid 36175685)
37. Bos KI, et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478(7370):506-510.
38. Knapp M, Hofreiter M (2010) Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes 1(2):227-243.
39. Sreevatsan S, et al. (1997) Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA 94(18):9869-9874. (Pubitemid 27408157)
40. Filliol I, et al. (2006) Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: Insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 188(2):759-772. (Pubitemid 43100562)
41. Gutierrez MC, et al. (2005) Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog 1(1):e5.
42. Huard RC, et al. (2006) Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol 188(12):4271-4287. (Pubitemid 43865747)
43. Gori A, Franzetti F, Marchetti G, Catozzi L, Corbellino M (1996) Specific detection of Mycobacterium tuberculosis by mtp40 nested PCR. J Clin Microbiol 34(11):2866-2867. (Pubitemid 26346524)
44. Liébana E, Aranaz A, Francis B, Cousins D (1996) Assessment of genetic markers for species differentiation within the Mycobacterium tuberculosis complex. J Clin Microbiol 34(4):933-938. (Pubitemid 26091510)
45. Weil A, Plikaytis BB, Butler WR, Woodley CL, Shinnick TM (1996) The mtp40 gene is not present in all strains of Mycobacterium tuberculosis. J ClinMicrobiol 34(9):2309-2311. (Pubitemid 26272227)
46. Koivula T, Svenson SB, Källenius G (2002) The mtp40 gene is not present in Mycobacterium bovis. Tuberculosis (Edinb) 82(4-5):183-185. (Pubitemid 35434272)
47. Ioerger TR, et al. (2010) Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories. J Bacteriol 192(14):3645-3653.
48. Marmiesse M, et al. (2004) Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex. Microbiology 150(Pt 2):483-496. (Pubitemid 38220052)
49. Cooper A, Poinar HN (2000) Ancient DNA: Do it right or not at all. Science 289(5482):1139. (Pubitemid 30650710)
50. Gilbert MTP, Bandelt H-J, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20(10):541-544. (Pubitemid 41323710)
51. Donoghue HD, Spigelman M (2006) Comment. Pathogenic microbial ancient DNA: A problem or an opportunity? Proc Biol Sci 273(1587):641-642. (Pubitemid 46780865)
52. Bouwman AS, Chilvers ER, Brown KA, Brown TA (2006) Brief communication: Identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA. Am J Phys Anthropol 131(3):428-431. (Pubitemid 44579705)
53. Konomi N, Lebwohl E, Mowbray K, Tattersall I, Zhang D (2002) Detection of mycobacterial DNA in Andean mummies. J Clin Microbiol 40(12):4738-4740. (Pubitemid 35434977)
54. Brimacombe M, Hazbon M, Motiwala AS, Alland D (2007) Antibiotic resistance and single-nucleotide polymorphism cluster grouping type in a multinational sample of resistant Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother 51(11):4157-4159. (Pubitemid 350057818)
55. Caffell AC, Holst M (2009) Osteological analysis. St. George's Crypt, Leeds, West Yorkshire. Report No 0409 (York Osteoarchaeology Ltd., Yorkshire, UK).
56. Roberts CA, Lucy D, Manchester K (1994) Inflammatory lesions of ribs: An analysis of the Terry Collection. Am J Phys Anthropol 95(2):169-182. (Pubitemid 24299026)
57. Bouwman AS, Brown TA (2005) The limits of biomolecular palaeopathology: Ancient DNA cannot be used to study venereal syphilis. J Archaeol Sci 32(5):703-713. (Pubitemid 40393602)
58. Camus JC, Pryor MJ, Médigue C, Cole ST (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148(Pt 10):2967-2973. (Pubitemid 35243696)
59. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
60. Goecks J, Nekrutenko A, Taylor J; Galaxy Team (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86.
61. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7(1-2):203-214. (Pubitemid 30412170)
62. Huson DH, Scornavacca C (2012) Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst Biol 10.1093/sysbio/sys062.
63. Rohland N, Siedel H, HofreiterM(2010) A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 10(4):677-683.
64. Rohland N, Hofreiter M (2007) Ancient DNA extraction from bones and teeth. Nat Protoc 2(7):1756-1762.