Application of FLiP method for differentiation of Mycobacterium tuberculosis strains in comparison to commonly used methods, spoligotyping and MIRU-VNTR typing

• Autorzy: Zaczek A. , Brzostek A. , Gorna A. , Sajduda A. , Wojtasik A. , Dziadek J.
• Języki publikacji: EN

Abstrakty

EN

The current “gold standard” in molecular epidemiological studies of Mycobacterium tuberculosis is IS6110 RFLP based on IS6110 polymorphism. However PCR-based methods are becoming increasingly important. Recently, fast ligation-mediated PCR (FLiP), based on IS6110 polymorphism was proposed. In this study, the discriminatory power of FLiP, spoligotyping and MIRU-VNTR typing, in differentiation of M. tuberculosis isolates was compared. The discriminatory index (HGI) of spoligotyping, MIRU-VNTR analysis, and FLiP was 0.653, 0.837, and 0.917, respectively. This indicates that FLiP allows a high level of differentiation among M. tuberculosis strains and it might be a valuable alternative to the other typing methods.

Słowa kluczowe

EN

application; FLiP method; strain differentiation; Mycobacterium tuberculosis; spoligotyping; MIRU-VNTR typing

• Wydawca: -
• Czasopismo: Polish Journal of Microbiology
• Rocznik: 2013
• Tom: 62
• Numer: 1
• Opis fizyczny: p.73-76,fig.,ref.

Twórcy

autor

Zaczek A.

• Department of Biochemistry and Cell Biology, University of Rzeszow, Poland

autor

Brzostek A.

• Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland

autor

Gorna A.

• Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
• Department of Genetic of Microorganisms, University of Lodz, Poland

autor

Sajduda A.

• Department of Genetic of Microorganisms, University of Lodz, Poland

autor

Wojtasik A.

• Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland

autor

Dziadek J.

• Department of Biochemistry and Cell Biology, University of Rzeszow, Poland
• Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland

Bibliografia

• Allix-Béguec C., D. Harmsen, T. Weniger, P. Supply and S. Niemann. 2008. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J. Clin. Microbial. 46: 2692–2699.
• Blackwood K.S., J.N. Wolfe and A.M. Kabani. 2004. Application of mycobacterial interspersed repetitive unit typing to Manitoba tuberculosis cases: can restriction fragment length polymorphism be forgotten? J. Clin. Microbiol. 42: 5001–5006.
• Covan L.S., L. Diem, T. Monson, P. Wand, D. Temporado, T.V. Oemig and J.T. Crawford. 2005. Evaluation of a two-step approach for large-scale, prospective genotyping of Mycobacterium tuberculosis isolates in the United States. J. Clin. Microbiol. 43: 688–695.
• Eisenach K.D., J.T. Crawford and J.H. Bates. 1988. Repetitive DNA sequences as probes for Mycobacterium tuberculosis. J. Clin. Microbiol. 26: 2240– 2245.
• Gutacker M.M., J.C. Smoot, C.A.L. 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.
• Hunter P.R. and M.A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J. Clin. Microbiol. 26: 2465–2466.
• Kamerbeek J., L. Schouls, A. Kolk, M. van Agterveld, D. van Soolingen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, M. Goyal and others. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35: 907–914.
• Krawczyk M., A. Brzostek, A. Gorna, K. Knapska, M. Ziolkiewicz, A. Wojtasik and J. Dziadek. 2011. Epidemiological analysis of Mycobacterium tuberculosis strains isolated in Lodz, Poland. Int. J. Tuberc. Lung Dis. 15: 1252–1258.
• Kremer K., C. Arnold, A. Cataldi, M.C. Gutiérrez, W.H. Haas, S. Panaiotov, R.A. Skuce, P. Supply, A.G.M. van der Zanden and D. van Soolingen. 1999a. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J. Clin. Microbiol. 43: 5628–5638.
• Kremer K., D. van Soolingen, R. Frothingham, W.H. Haas, P.W. Hermans, C. Martín, P. Palittapongarnpim, B.B. Plikaytis, L.W. Riley, M.A. Yakrus, J.M. Musser and J.D. van Embden. 1999b. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J. Clin. Microbiol. 37: 2607–2618.
• Maes M., K. Kremer, D. van Soolingen, H. Takiff and J.H. de Waard. 2008. 24-locus MIRU-VNTR genotyping is a useful tool to study the molecular epidemiology of tuberculosis among Warao Amerindians in Venezuela. Tuberculosis 5: 490–494.
• 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.
• Reisig, F., K. Kremer, B. Amthor, D. van Soolingen and W.H. Haas. 2005. Fast ligation-mediated PCR, a fast and reliable method for IS6110-based typing of Mycobacterium tuberculosis complex. J. Clin. Microbiol. 43: 5622–5627.
• Sajduda A., J. Dziadek, R. Kotłowski and F. Portaels. 2006. Evaluation of multiple genetic markers for typing drug-resistant Mycobacterium tuberculosis strains from Poland. Diagn. Microbiol. Infect. Dis. 55: 59–64.
• Supply P., C. Allix, S. Lejean, M. Cardosso-Oelemann, S. Rush-Gerdes, E. Willery, E. Savine, P. de Haas, H. van Deutekom, S. Roring and others. 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J. Clin. Microbiol. 44: 4498–4510.
• Thierry D., M.D. Cave, K.D. Eisenach J. T Crawford, J.H. Bates, B. Gicquel and J. L. Guesdon. 1990. IS6110, an IS-like element of Mycobacterium tuberculosis complex. Nucleic Acids Res. 18: 188–193.
• van Embden J.D., M.D. Cave, J.T. Crawford, J.W. Dale, K.D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam and T. Shinnick. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31: 406–409.
• Van Soolingen D., K. Kremer and E. Vynnycky. 2003. New perspectives in the molecular epidemiology of tuberculosis. Mycobacteria and TB. 2: 17–45.