Population-based study of deletions in five different genomic regions of Mycobacterium tuberculosis and possible clinical relevance of the deletions

Journal of Clinical Microbiology

Volumn 44, Issue 11, 2006, Pages 3940-3946

  Kong, Y ^a   Cave, M D ^b,c   Zhang, L ^a   Foxman, B ^a   Marrs, C F ^a   Bates, J H ^d,e   Yang, Z H ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b CENTRAL ARKANSAS VETERANS HEALTHCARE SYSTEM   (United States)

^c UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^d UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^e ARKANSAS DEPARTMENT OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; CHI SQUARE TEST; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; EXTRAPULMONARY TUBERCULOSIS; GENDER; GENE; GENE DELETION; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAJOR CLINICAL STUDY; MULTIVARIATE LOGISTIC REGRESSION ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLCD GENE; POLYMERASE CHAIN REACTION; POPULATION RESEARCH; PRIORITY JOURNAL; RACE; RISK FACTOR; STATISTICAL SIGNIFICANCE;

ADOLESCENT; ADULT; AGED; CHILD; CHILD, PRESCHOOL; GENE DELETION; GENOME, BACTERIAL; GENOTYPE; HUMANS; INFANT; INFANT, NEWBORN; LOGISTIC MODELS; MIDDLE AGED; MYCOBACTERIUM TUBERCULOSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION;

HUMAN IMMUNODEFICIENCY VIRUS; MYCOBACTERIUM TUBERCULOSIS;

EID: 33750944979     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01146-06     Document Type: Article

References (29)

1. Anh, D. D., M. W. Borgdorff, L. N. Van, N. T. Lan, T. van Gorkom, K. Kremer, and D. van Soolingen. 2000. Mycobacterium tuberculosis Beijing genotype emerging in Vietnam. Emerg. Infect. Dis. 6:302-305.
2. Barnes, P. F., Z. Yang, S. Preston-Martin, J. M. Pogoda, B. E. Jones, M. Otaya, K. D. Eisenach, L. Knowles, S. Harvey, and M. D. Cave. 1997. Patterns of tuberculosis transmission in central Los Angeles. JAMA 278:1159-1163.
3. Bifani, P. J., B. Mathema, N. E. Kurepina, and B. N. Kreiswirth. 2002. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol. 10:45-52.
4. Boddinghaus, B., T. Rogall, T. Flohr, H. Blocker, and E. C. Bottger. 1990. Detection and identification of mycobacteria by amplification of rRNA. J. Clin. Microbiol. 28:1751-1759.
5. Braden, C. R., G. L. Templeton, M. D. Cave, S. Valway, I. M. Onorato, K. G. Castro, D. Moers, Z. Yang, W. W. Stead, and J. H. Bates. 1997. Interpretation of restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates from a state with a large rural population. J. Infect. Dis. 175:1446-1452.
6. Chaves, F., Z. Yang, H. el Hajj, M. Alonso, W. J. Burman, K. D. Eisenach, F. Dronda, J. H. Bates, and M. D. Cave. 1996. Usefulness of the secondary probe pTBN12 in DNA fingerprinting of Mycobacterium tuberculosis. J. Clin. Microbiol. 34:1118-1123.
7. Dale, J. W., R. M. Nor, S. Ramayah, T. H. Tang, and Z. F. Zainuddin. 1999. Molecular epidemiology of tuberculosis in Malaysia. J. Clin. Microbiol. 37:1265-1268.
8. 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 phytogeny 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.
9. 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.
10. 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.
11. Hirsh, A. E., A. G. Tsolaki, K. DeRiemer, M. W. Feldman, and P. M. Small. 2004. From the cover: stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc. Natl. Acad. Sci. USA 101:4871-4876.
12. Hughes, A. L., R. Friedman, and M. Murray. 2002. Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis. Emerg. Infect. Dis. 8:1342-1346.
13. Kong, Y., M. D. Cave, D. Yang, L. Zhang, C. F. Marrs, B. Foxman, J. H. Bates, F. Wilson, L. N. Mukasa, and Z. H. Yang. 2005. Distribution of insertion- and deletion-associated genetic polymorphisms among four Mycobacterium tuberculosis phospholipase C genes and associations with extrathoracic tuberculosis: a population-based study. J. Clin. Microbiol. 43:6048-6053.
14. Kremer, K., J. R. Glynn, T. Lillebaek, S. Niemann, N. E. Kurepina, B. N. Kreiswirth, P. J. Bifani, and D. van Soolingen. 2004. Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers. J. Clin. Microbiol. 42:4040-4049.
15. Liang, K., and S. L. Zeger. 1986. Longitudinal data analysis using generalized linear models. Biometrika 73:13-22.
16. Manca, C., L. Tsenova, C. E. Barry III, A. Bergtold, S. Freeman, P. A. Haslett, J. M. Musser, V. H. Freedman, and G. Kaplan. 1999. Mycobacterium tuberculosis CDC1551 induces a more vigorous host response in vivo and in vitro, but is not more virulent than other clinical isolates. J. Immunol. 162:6740-6746.
17. Manganelli, R., R. Proveddi, S. Rodrigue, J. Beaucher, L. Gaudreau, and I. Smith. 2004. Sigma factors and global gene regulation in Mycobacterium tuberculosis. J. Bacteriol, 186:895-902.
18. Murray, M. G., and W. F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321-4325.
19. 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.
20. Tsolaki, A. G., S. Cagneux, A. S. Pym, Y. O. Goguet de la Salmoniere, B. N. Kreiswirth, D. Van Soolingen, and P. M. Small. 2005. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J. Clin. Microbiol. 43:3185-3191.
21. 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.
22. Valway, S. E., M. P. Sanchez, T. F. Shinnick, I. Orme, T. Agerton, D. Hoy, J. S. Jones, H. Westmorland, and I. M. Onorato. 1998. An outbreak involving extensive transmission of a virulent strain of Mycobacterium tuberculosis. N. Engl. J. Med. 338:633-639.
23. van Embden, J. D., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:400-409.
24. van Soolingen, D., L. Qian, P. E. de Haas, J. T. Douglas, H. Traoce, F. Portaels, H. Z. Qing, D. Enkhsaikan, P. Nymadawa, and J. O. van Embden. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J. Clin. Microbioi. 33:3234-3238.
25. Vynnycky, E., N. Nageifeecke, M. W. Borgdorft D. van Soolingen, J. D. van Embden, and P. E. Fine. 2001. The effect of age and study duration on the relationship between 'clustering' of DNA fingerprint patterns and the proportion of tuberculosis disease attributable to recent transmission. Epidemiol. Infect. 126:43-62.
26. Yang, Z., Y. Kong, F. Wilson, B. Foxman, A. H. Fowler, C. P. Marrs, M. D. Cave, and J. H. Bates. 2004. Identification of risk factors for extrapulmonary tubercuiosis. Clin. Infect. Dis. 38:199-205.
27. 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 Mycabacterium tuberculosis plcD gene mutations. Am. J. Respir. Crit. Care Med. 171:1436-1442.
28. Zeger, S. L., and K. Liang. 1986. Longitudinal data analysis for discrete and continuous outcomes. Biometrics 42:121-130.
29. Zhang, L., V. Srinivasan, C. F. Marrs, D. Ghosh, J. R. Gilsdorf, and B. Foxman. 2004. Library on a slide fot bacterial comparative genomics. BMC Microbiol. 4:12.