Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis

Journal of Clinical Microbiology

Volumn 45, Issue 1, 2007, Pages 39-46

  Alland, David ^a,d   Lacher, David W ^b   Hazbón, Manzour Hernando ^a   Motiwala, Alifiya S ^a   Qi, Weihong ^b   Fleischmann, Robert D ^c   Whittam, Thomas S ^b  

^a RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; GLUTAMIC ACID; PROLINE;

ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; GENE DELETION; GENE INSERTION; GENE MAPPING; GENETIC POLYMORPHISM; GENETIC VARIABILITY; LARGE SEQUENCE POLYMORPHISM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE DELETION; GENOME, BACTERIAL; HUMANS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

MYCOBACTERIUM TUBERCULOSIS;

EID: 33846195782     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.02483-05     Document Type: Article

References (34)

1. Alland, D., G. E. Kalkut, A. R. Moss, R. A. McAdam, J. A. Hahn, W. Bosworth, E. Drucker, and B. R. Bloom. 1994. Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods. N. Engl. J. Med. 330:1710-1716.
2. Alland, D., T. S. Whittam, M. B. Murray, M. D. Cave, M. H. Hazbon, K. Dix, M. Kokons, A. Duesterhoeft, J. A. Eisen, C. M. Fraser, and R. D. Fleischmann. 2003. Modeling bacterial evolution with comparative-genome- based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J. Bacteriol. 185:3392-3399.
3. Baek, S. H., G. Rajashekara, G. A. Splitter, and J. P. Shapleigh. 2004. Denitrification genes regulate Brucella virulence in mice. J. Bacteriol. 186:6025-6031.
4. Blaser, M. J., and J. C. Atherton. 2004. Helicobacter pylori persistence: biology and disease. J. Clin. Investig. 113:321-333.
5. Brosch, R., W. J. Philipp, E. Stavropoulos, M. J. Colston, S. T. Cole, and S. V. Gordon. 1999. Genomic analysis reveals variation between Mycobacterium tuberculosis H37Rv and the attenuated M. tuberculosis H37Ra strain. Infect. Immun. 67:5768-5774.
6. Choudhary, R. K., R. Pullakhandam, N. Z. Ehtesham, and S. E. Hasnain. 2004. Expression and characterization of Rv2430c, a novel immunodominant antigen of Mycobacterium tuberculosis. Protein Expr. Purif. 36:249-253.
7. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M. A. Quail, M. A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
8. Day, W. A., Jr., R. E. Fernandez, and A. T. Maurelli. 2001. Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infect. Immun. 69:7471-7480.
9. Delogu, G., and M. J. Brennan. 2001. Comparative immune response to PE and PE_PGRS antigens of Mycobacterium tuberculosis. Infect. Immun. 69:5606-5611.
10. de Visser, J. A., A. D. Akkermans, R. F. Hoekstra, and W. M. de Vos. 2004. Insertion-sequence-mediated mutations isolated during adaptation to growth and starvation in Lactococcus lactis. Genetics 168:1145-1157.
11. Ernst, R. K., D. A. D'Argenio, J. K. Ichikawa, M. G. Bangera, S. Selgrade, J. L. Burns, P. Hiatt, K. McCoy, M. Brittnacher, A. Kas, D. H. Spencer, M. V. Olson, B. W. Ramsey, S. Lory, and S. I. Miller. 2003. Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis. Environ Microbiol. 5:1341-1349.
12. Espitia, C., J. P. Laclette, M. Mondragon-Palomino, A. Amador, J. Campuzano, A. Martens, M. Singh, R. Cicero, Y. Zhang, and C. Moreno. 1999. The PE-PGRS glycine-rich proteins of Mycobacterium tuberculosis: a new family of fibronectin-binding proteins? Microbiology 145:3487-3495.
13. Fang, Z., C. Doig, D. T. Kenna, N. Smittipat, P. Palittapongarnpim, B. Watt, and K. J. Forbes. 1999. IS6110-mediated deletions of wild-type chromosomes of Mycobacterium tuberculosis. J. Bacteriol. 181:1014-1020.
14. Fang, Z., and K. J. Forbes. 1997. A Mycobacterium tuberculosis IS6110 preferential locus (ipl) for insertion into the genome. J. Clin. Microbiol. 35:479-481.
15. 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.
16. Fleischmann, R. D., D. Alland, J. A. Eisen, L. Carpenter, O. White, J. Peterson, R. DeBoy, R. Dodson, M. Gwinn, D. Haft, E. Hickey, J. F. Kolonay, W. C. Nelson, L. A. Umayam, M. Ermolaeva, S. L. Salzberg, A. Delcher, T. Utterback, J. Weidman, H. Khouri, J. Gill, A. Mikula, W. Bishai, W. R. Jacobs, Jr., J. C. Venter, and C. M. Fraser. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184:5479-5490.
17. Gagneux, S., K. DeRiemer, T. Van, M. Kato-Maeda, B. C. de Jong, S. Narayanan, M. Nicol, S. Niemann, K. Kremer, M. C. Gutierrez, M. Hilty, P. C. Hopewell, and P. M. Small. 2006. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103:2869-2873.
18. Gao, Q., K. E. Kripke, A. J. Saldanha, W. Yan, S. Holmes, and P. M. Small. 2005. Gene expression diversity among Mycobacterium tuberculosis clinical isolates. Microbiology 151:5-14.
19. Goerke, C., S. Matias y Papenberg, S. Dasbach, K. Dietz, R. Ziebach, B. C. Kahl, and C. Wolz. 2004. Increased frequency of genomic alterations in Staphylococcus aureus during chronic infection is in part due to phage mobilization. J. Infect. Dis. 189:724-734.
20. Goguet de la Salmoniere, Y. O., C. C. Kim, A. G. Tsolaki, A. S. Pym, M. S. Siegrist, and P. M. Small. 2004. High-throughput method for detecting genomic-deletion polymorphisms. J. Clin. Microbiol. 42:2913-2918.
21. Gomez-Valero, L., A. Latorre, and F. J. Silva. 2004. The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol. Biol Evol. 21:2172-2181.
22. Hazbon, M. H., and D. Alland. 2004. Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms. J. Clin. Microbiol. 42:1236-1242.
23. 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.
24. Ho, T. B., B. D. Robertson, G. M. Taylor, R. J. Shaw, and D. B. Young. 2000. Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast 17:272-282.
25. Israel, D. A., N. Salama, C. N. Arnold, S. F. Moss, T. Ando, H. P. Wirth, K. T. Tham, M. Camorlinga, M. J. Blaser, S. Falkow, and R. M. Peek, Jr. 2001. Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. J. Clin. Investig. 107:611-620.
26. 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.
27. Kuipers, E. J., D. A. Israel, J. G. Kusters, M. M. Gerrits, J. Weel, A. van Der Endeqq, R. W. van Der Hulstqq, H. P. Wirth, J. Hook-Nikanne, S. A. Thompson, and M. J. Blaser. 2000. Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J. Infect. Dis. 181:273-282.
28. 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.
29. Pearson, B. M., C. Pin, J. Wright, K. I'Anson, T. Humphrey, and J. M. Wells. 2003. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett. 554:224-230.
30. Sampson, S. L., M. Richardson, P. D. Van Helden, and R. M. Warren. 2004. IS6110-mediated deletion polymorphism in isogenic strains of Mycobacterium tuberculosis. J. Clin. Microbiol. 42:895-898.
31. Sreevatsan, S., X. Pan, K. E. Stockbauer, N. D. Connell, B. N. Kreiswirth, T. S. Whittam, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:9869-9874.
32. 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.
33. Yang, Z., D. Yang, Y. Kong, L. Zhang, C. F. Marrs, B. Foxman, J. H. Bates, F. Wilson, and M. D. Cave. 2005. Clinical relevance of Mycobacterium tuberculosis plcD gene mutations. Am. J. Respir. Crit. Care Med. 171:1436-1442.
34. Zhong, S., A. Khodursky, D. E. Dykhuizen, and A. M. Dean. 2004. Evolutionary genomics of ecological specialization. Proc. Natl. Acad. Sci. USA 101:11719-11724.