Lack of insertional-deletional polymorphism in a collection of Mycobacterium ulcerans isolates from Ghanaian Buruli ulcer patients

Journal of Clinical Microbiology

Volumn 47, Issue 11, 2009, Pages 3640-3646

  Käser, Michael ^a   Gutmann, Oliver ^b   Hauser, Julia ^a   Stinear, Tim ^c   Cole, Stewart ^d   Yeboah Manu, Dorothy ^e   Dernick, Gregor ^b   Certa, Ulrich ^b   Pluschke, Gerd ^a  

^a SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

^c MONASH UNIVERSITY   (Australia)

^d EPFL   (Switzerland)

^e University of Ghana   (Ghana)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BURULI ULCER; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; HUMAN; INDEL MUTATION; MYCOBACTERIUM ULCERANS; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

BURULI ULCER; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, BACTERIAL; ENDEMIC DISEASES; GHANA; HUMANS; INDEL MUTATION; MYCOBACTERIUM ULCERANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC;

MYCOBACTERIUM ULCERANS;

EID: 70449659277     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00760-09     Document Type: Article

References (63)

1. Ablordey, A., P. A. Fonteyne, P. Stragier, P. Vandamme, and F. Portaels. 2007. Identification of a new variable number tandem repeat locus in Mycobacterium ulcerans for potential strain discrimination among African isolates. Clin. Microbiol. Infect. 13:734-736.
2. Ablordey, A., M. Hilty, P. Stragier, J. Swings, and F. Portaels. 2005. Comparative nucleotide sequence analysis of polymorphic variable-number tandem-repeat Loci in Mycobacterium ulcerans. J. Clin. Microbiol. 43:5281-5284. (Pubitemid 41484039)
3. Ablordey, A., R. Kotlowski, J. Swings, and F. Portaels. 2005. PCR amplification with primers based on IS2404 and GC-rich repeated sequence reveals polymorphism in Mycobacterium ulcerans. J. Clin. Microbiol. 43:448-451. (Pubitemid 40096341)
4. Ablordey, A., J. Swings, C. Hubans, K. Chemlal, C. Locht, F. Portaels, and P. Supply. 2005. Multilocus variable-number tandem repeat typing of Mycobacterium ulcerans. J. Clin. Microbiol. 43:1546-1551.
5. Alland, D., D. W. Lacher, M. H. Hazbon, A. S. Motiwala, W. Qi, R. D. Fleischmann, and T. S. Whittam. 2007. Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. J. Clin. Microbiol. 45:39-46.
6. Behr, M. A., M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523. (Pubitemid 129524431)
7. Brosch, R., S. V. Gordon, T. Garnier, K. Eiglmeier, W. Frigui, P. Valenti, S. S. Dos, S. Duthoy, C. Lacroix, C. Garcia-Pelayo, J. K. Inwald, P. Golby, J. N. Garcia, R. G. Hewinson, M. A. Behr, M. A. Quail, C. Churcher, B. G. Barrell, J. Parkhill, and S. T. Cole. 2007. Genome plasticity of BCG and impact on vaccine efficacy. Proc. Natl. Acad. Sci. USA 104:5596-5601.
8. Brosch, R., S. V. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser, K. Eiglmeier, T. Garnier, C. Gutierrez, G. Hewinson, K. Kremer, L. M. Parsons, A. S. Pym, S. Samper, D. van Soolingen, and S. T. Cole. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. USA 99:3684-3689.
9. Brosch, R., A. S. Pym, S. V. Gordon, and S. T. Cole. 2001. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9:452-458. (Pubitemid 32844332)
10. Chemlal, K., K. De Ridder, P. A. Fonteyne, W. M. Meyers, J. Swings, and F. Portaels. 2001. The use of IS2404 restriction fragment length polymorphisms suggests the diversity of Mycobacterium ulcerans from different geographical areas. Am. J. Trop. Med. Hyg. 64:270-273.
11. Chemlal, K., G. Huys, P. A. Fonteyne, V. Vincent, A. G. Lopez, L. Rigouts, J. Swings, W. M. Meyers, and F. Portaels. 2001. Evaluation of PCR-restriction profile analysis and IS2404 restriction fragment length polymorphism and amplified fragment length polymorphism fingerprinting for identification and typing of Mycobacterium ulcerans and M. marinum. J. Clin. Microbiol. 39:3272-3278. (Pubitemid 32830326)
12. Cole, S. T. 2002. Comparative and functional genomics of the Mycobacterium tuberculosis complex. Microbiology 148:2919-2928.
13. Debacker, M., F. Portaels, J. Aguiar, C. Steunou, C. Zinsou, W. Meyers, and M. Dramaix. 2006. Risk factors for Buruli ulcer, Benin. Emerg. Infect. Dis. 12:1325-1331.
14. Demangel, C., T. P. Stinear, and S. T. Cole. 2009. Buruli ulcer: reductive evolution enhances pathogenicity of Mycobacterium ulcerans. Nat. Rev. Microbiol. 7:50-60.
15. Diaz, R., N. Siddiqi, and E. J. Rubin. 2006. Detecting genetic variability among different Mycobacterium tuberculosis strains using DNA microarrays technology. Tuberculosis 86:314-318.
16. Filliol, I., A. S. Motiwala, M. Cavatore, W. Qi, M. H. Hazbon, M. Bobadilla del Valle, J. Fyfe, L. Garcia-Garcia, N. Rastogi, C. Sola, T. Zozio, M. I. Guerrero, C. I. Leon, J. Crabtree, S. Angiuoli, K. D. Eisenach, R. Durmaz, M. L. Joloba, A. Rendon, J. Sifuentes-Osornio, A. Ponce de Leon, M. D. Cave, R. Fleischmann, T. S. Whittam, and D. Alland. 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. 188:759-772.
17. Gagneux, S., and P. M. Small. 2007. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect. Dis. 7:328-337.
18. Garcia-Pelayo, M. C., K. C. Caimi, J. K. Inwald, J. Hinds, F. Bigi, M. I. Romano, D. van Soolingen, R. G. Hewinson, A. Cataldi, and S. V. Gordon. 2004. Microarray analysis of Mycobacterium microti reveals deletion of genes encoding PE-PPE proteins and ESAT-6 family antigens. Tuberculosis (Edinb.) 84:159-166.
19. Gordon, S. V., R. Brosch, A. Billault, T. Garnier, K. Eiglmeier, and S. T. Cole. 1999. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol. Microbiol. 32:643-655.
20. Grietens, K. P., A. U. Boock, H. Peeters, S. Hausmann-Muela, E. Toomer, and J. M. Ribera. 2008. "It is me who endures but my family that suffers": social isolation as a consequence of the household cost burden of Buruli ulcer free of charge hospital treatment. PLoS Negl. Trop. Dis. 2:e321.
21. Gutacker, M. M., B. Mathema, H. Soini, E. Shashkina, B. N. Kreiswirth, E. A. Graviss, and J. M. Musser. 2006. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites. J. Infect. Dis. 193:121-128.
22. Gutacker, M. M., J. C. Smoot, C. A. Migliaccio, S. M. Ricklefs, S. Hua, D. V. Cousins, E. A. Graviss, E. Shashkina, B. N. Kreiswirth, and J. M. Musser. 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 162:1533-1543.
23. Hilty, M., M. Kaser, J. Zinsstag, T. Stinear, and G. Pluschke. 2007. Analysis of the Mycobacterium ulcerans genome sequence reveals new loci for variable number tandem repeats (VNTR) typing. Microbiology 153:1483-1487.
24. Hilty, M., D. Yeboah-Manu, D. Boakye, E. Mensah-Quainoo, S. Rondini, E. Schelling, D. Ofori-Adjei, F. Portaels, J. Zinsstag, and G. Pluschke. 2006. Genetic diversity in Mycobacterium ulcerans isolates from Ghana revealed by a newly identified locus containing a variable number of tandem repeats. J. Bacteriol. 188:1462-1465.
25. Hirsh, A. E., A. G. Tsolaki, K. DeRiemer, M. W. Feldman, and P. M. Small. 2004. Stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc. Natl. Acad. Sci. USA 101:4871-4876.
26. Huber, C. A., M. T. Ruf, G. Pluschke, and M. Kaser. 2008. Independent loss of immunogenic proteins in Mycobacterium ulcerans suggests immune evasion. Clin. Vaccine Immunol. 15:598-606.
27. Kaser, M., J. Hauser, P. Small, and G. Pluschke. 2009. Large sequence polymorphisms unveil the phylogenetic relationship of environmental and pathogenic mycobacteria related to Mycobacterium ulcerans. Appl. Environ. Microbiol. 75:5667-5675.
28. Kaser, M., and G. Pluschke. 2008. Differential gene repertoire in Mycobacterium ulcerans identifies candidate genes for patho-adaptation. PLoS Negl. Trop. Dis. 2:e353.
29. Kaser, M., S. Rondini, M. Naegeli, T. Stinear, F. Portaels, U. Certa, and G. Pluschke. 2007. Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans. BMC Evol. Biol. 7:177.
30. Kaser, M., M. T. Ruf, J. Hauser, L. Marsollier, and G. Pluschke. 2009. Optimized method for preparation of DNA from pathogenic and environmental mycobacteria. Appl. Environ. Microbiol. 75:414-418.
31. Käser, M., J. Hauser, and G. Pluschke. 2009. Single nucleotide polymorphisms on the road to strain differentiation in Mycobacterium ulcerans. J. Clin. Microbiol. 47:3647-3652.
32. Kato-Maeda, M., J. T. Rhee, T. R. Gingeras, H. Salamon, J. Drenkow, N. Smittipat, and P. M. Small. 2001. Comparing genomes within the species Mycobacterium tuberculosis. Genome Res. 11:547-554.
33. Lavender, C. J., T. P. Stinear, P. D. Johnson, J. Azuolas, M. E. Benbow, J. R. Wallace, and J. A. Fyfe. 2008. Evaluation of VNTR typing for the identification of Mycobacterium ulcerans in environmental samples from Victoria, Australia. FEMS Microbiol. Lett. 287:250-255.
34. Malik, A. N., and P. Godfrey-Faussett. 2005. Effects of genetic variability of Mycobacterium tuberculosis strains on the presentation of disease. Lancet Infect. Dis. 5:174-183.
35. Marsh, I. B., J. P. Bannantine, M. L. Paustian, M. L. Tizard, V. Kapur, and R. J. Whittington. 2006. Genomic comparison of Mycobacterium avium subsp. paratuberculosis sheep and cattle strains by microarray hybridization. J. Bacteriol. 188:2290-2293.
36. Marsollier, L., R. Robert, J. Aubry, J. P. Saint Andre, H. Kouakou, P. Legras, A. L. Manceau, C. Mahaza, and B. Carbonnelle. 2002. Aquatic insects as a vector for Mycobacterium ulcerans. Appl. Environ. Microbiol. 68:4623-4628.
37. Mathema, B., N. E. Kurepina, P. J. Bifani, and B. N. Kreiswirth. 2006. Molecular epidemiology of tuberculosis: current insights. Clin. Microbiol. Rev. 19:658-685.
38. Mostowy, S., D. Cousins, J. Brinkman, A. Aranaz, and M. A. Behr. 2002. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J. Infect. Dis. 186:74-80.
39. Mostowy, S., J. Inwald, S. Gordon, C. Martin, R. Warren, K. Kremer, D. Cousins, and M. A. Behr. 2005. Revisiting the evolution of Mycobacterium bovis. J. Bacteriol. 187:6386-6395.
40. Mostowy, S., A. Onipede, S. Gagneux, S. Niemann, K. Kremer, E. P. Desmond, M. Kato-Maeda, and M. Behr. 2004. Genomic analysis distinguishes Mycobacterium africanum. J. Clin. Microbiol. 42:3594-3599.
41. Mve-Obiang, A., R. E. Lee, F. Portaels, and P. L. Small. 2003. Heterogeneity of mycolactones produced by clinical isolates of Mycobacterium ulcerans: implications for virulence. Infect. Immun. 71:774-783.
42. Paustian, M. L., V. Kapur, and J. P. Bannantine. 2005. Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates. J. Bacteriol. 187:2406-2415.
43. Paustian, M. L., X. Zhu, S. Sreevatsan, S. Robbe-Austerman, V. Kapur, and J. P. Bannantine. 2008. Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species. BMC Genomics 9:135.
44. Portaels, F., P. Elsen, A. Guimaraes-Peres, P. A. Fonteyne, and W. M. Meyers. 1999. Insects in the transmission of Mycobacterium ulcerans infection. Lancet 353:986.
45. Pouillot, R., G. Matias, C. M. Wondje, F. Portaels, N. Valin, F. Ngos, A. Njikap, L. Marsollier, A. Fontanet, and S. Eyangoh. 2007. Risk factors for Buruli ulcer: a case control study in Cameroon. PLoS Negl. Trop. Dis. 1:e101.
46. Quek, T. Y., E. Athan, M. J. Henry, J. A. Pasco, J. Redden-Hoare, A. Hughes, and P. D. Johnson. 2007. Risk factors for Mycobacterium ulcerans infection, southeastern Australia. Emerg. Infect. Dis. 13:1661-1666.
47. Rondini, S., M. Käser, T. Stinear, M. Tessier, C. Mangold, G. Dernick, M. Naegeli, F. Portaels, U. Certa, and G. Pluschke. 2007. Ongoing genome reduction in Mycobacterium ulcerans. Emerg. Infect. Dis. 13:1008-1015.
48. Semret, M., G. Zhai, S. Mostowy, C. Cleto, D. Alexander, G. Cangelosi, D. Cousins, D. M. Collins, D. van Soolingen, and M. A. Behr. 2004. Extensive genomic polymorphism within Mycobacterium avium. J. Bacteriol. 186:6332-6334.
49. Sizaire, V., F. Nackers, E. Comte, and F. Portaels. 2006. Mycobacterium ulcerans infection: control, diagnosis, and treatment. Lancet Infect. Dis. 6:288-296.
50. Smith, N. H., S. V. Gordon, R. Rua-Domenech, R. S. Clifton-Hadley, and R. G. Hewinson. 2006. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat. Rev. Microbiol. 4:670-681.
51. Stinear, T., J. K. Davies, G. A. Jenkin, F. Portaels, B. C. Ross, F. Oppedisano, M. Purcell, J. A. Hayman, and P. D. Johnson. 2000. A simple PCR method for rapid genotype analysis of Mycobacterium ulcerans. J. Clin. Microbiol. 38:1482-1487.
52. Stinear, T. P., H. Hong, W. Frigui, M. J. Pryor, R. Brosch, T. Garnier, P. F. Leadlay, and S. T. Cole. 2005. Common evolutionary origin for the unstable virulence plasmid pMUM found in geographically diverse strains of Mycobacterium ulcerans. J. Bacteriol. 187:1668-1676.
53. Stinear, T. P., G. A. Jenkin, P. D. Johnson, and J. K. Davies. 2000. Comparative genetic analysis of Mycobacterium ulcerans and Mycobacterium marinum reveals evidence of recent divergence. J. Bacteriol. 182:6322-6330.
54. Stinear, T. P., T. Seemann, S. Pidot, W. Frigui, G. Reysset, T. Garnier, G. Meurice, D. Simon, C. Bouchier, L. Ma, M. Tichit, J. L. Porter, J. Ryan, P. D. Johnson, J. K. Davies, G. A. Jenkin, P. L. Small, L. M. Jones, F. Tekaia, F. Laval, M. Daffe, J. Parkhill, and S. T. Cole. 2007. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 17:192-200.
55. Stragier, P., A. Ablordey, L. M. Bayonne, Y. L. Lugor, I. S. Sindani, P. Suykerbuyk, H. Wabinga, W. M. Meyers, and F. Portaels. 2006. Heterogeneity among Mycobacterium ulcerans isolates from Africa. Emerg. Infect. Dis. 12:844-847.
56. Stragier, P., A. Ablordey, L. Durnez, and F. Portaels. 2007. VNTR analysis differentiates Mycobacterium ulcerans and IS2404 positive mycobacteria. Syst. Appl. Microbiol. 30:525-530.
57. Stragier, P., A. Ablordey, W. M. Meyers, and F. Portaels. 2005. Genotyping Mycobacterium ulcerans and Mycobacterium marinum by using mycobacterial interspersed repetitive units. J. Bacteriol. 187:1639-1647.
58. Tsolaki, A. G., A. E. Hirsh, K. DeRiemer, J. A. Enciso, M. Z. Wong, M. Hannan, Y. O. Goguet de la Salmoniere, K. Aman, M. Kato-Maeda, and P. M. Small. 2004. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc. Natl. Acad. Sci. USA 101:4865-4870.
59. Wagner, T., M. E. Benbow, T. O. Brenden, J. Qi, and R. C. Johnson. 2008. Buruli ulcer disease prevalence in Benin, West Africa: associations with land use/cover and the identification of disease clusters. Int. J. Health Geogr. 7:25.
60. Wansbrough-Jones, M., and R. Phillips. 2006. Buruli ulcer: emerging from obscurity. Lancet 367:1849-1858.
61. World Health Organization. 2008. Buruli ulcer: progress report, 2004-2008. Wkly. Epidemiol. Rec. 83:145-156.
62. Yeboah-Manu, D., T. Bodmer, E. Mensah-Quainoo, S. Owusu, D. Ofori-Adjei, and G. Pluschke. 2004. Evaluation of decontamination methods and growth media for primary isolation of Mycobacterium ulcerans from surgical specimens. J. Clin. Microbiol. 42:5875-5876.
63. Yip, M. J., J. L. Porter, J. A. Fyfe, C. J. Lavender, F. Portaels, M. Rhodes, H. Kator, A. Colorni, G. A. Jenkin, and T. Stinear. 2007. Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J. Bacteriol. 189:2021-2029.