A novel method of Mycobacterium tuberculosis complex strain differentiation using polymorphic GC-rich gene sequences

• Authors: Roman Kotłowski
• Languages of publication: EN

Abstracts

EN

Tuberculosis is one of the leading infectious diseases. In this work, a new genotyping method of Mycobacterium tuberculosis (Mtb) complex strain is presented. 27 Mtb genomes were analyzed for the presence of length polymorphism within polymorphic GC-rich gene sequences. Four genes, Rv3345c, Rv3507, Rv0747 and Rv3511, showing variation in length depending on the Mtb strain were selected for designing primer sequences flanking variable regions for the PCR method. Identification of 16 genotypes among 27 analyzed genomes demonstrated usefulness of our genotyping method in differentiation of Mtb genomes based on sequence polymorphism in the four PGRS genes.

Keywords

EN

Mycobacterium tuberculosis complex; PGRS; genotyping

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 2
• Pages: 317-322

Dates

published

2015

received

2015-04-23

revised

2015-05-21

accepted

2015-05-26

(unknown)

2015-06-22

Contributors

author

Roman Kotłowski

• Department of Molecular Biotechnology and Microbiology, Gdansk University of Technology, Gdańsk, Poland

References

• van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM, Small PM (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31: 406-409.
• Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907-914.
• Supply P, Lesjean S, Savine E, Kremer K, van Soolingen D, Locht C (2001) Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J Clin Microbiol 39: 3563-3571.
• Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Grosset J, Broman KW, Bishai WR (2003) A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 100: 7213-7218.
• Banu S, Honore N, Saint-Joanis B, Philpott D, Prevost MC, Cole ST (2002) Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol Microbiol 44: 9-19.
• Delogu G, Pusceddu C, Bua A, Fadda G, Brennan MJ, Zanetti S (2004) Rv1818c-encoded PE_PGRS protein of Mycobacterium tuberculosis is surface exposed and influences bacterial cell structure. Mol Microbiol 52: 725-733.
• Brennan MJ, Delogu G (2002) The PE multigene family: A 'molecular mantra' for mycobacteria. Trends Microbiol 10: 246-249.
• Brennan MJ, Delogu G, Chen Y, Bardarov S, Kriakov J, Alavi M, Jacobs WR Jr (2001) Evidence that mycobacterial PE_PGRS proteins are cell surface constituents that influence interactions with other cells. Infect Immun 69: 7326-7333.
• Delogu G, Brennan MJ (2001) Comparative immune response to PE and PE_PGRS antigens of Mycobacterium tuberculosis. Infect Immun 69: 5606-5611.
• Singh KK, Zhang X, Patibandla AS, Chien P Jr, Laal S (2001) Antigens of Mycobacterium tuberculosis expressed during preclinical tuberculosis: Serological immunodominance of proteins with repetitive amino acid sequences. Infect Immun 69: 4185-4191.
• Talarico S, Cave MD, Marrs CF, Foxman B, Zhang L, Yang Z (2005) Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates. J Clin Microbiol 43: 4954-4960.
• Chaitra MG, Hariharaputran S, Chandra NR, Shaila MS, Nayak R (2005) Defining putative T cell epitopes from PE and PPE families of proteins of Mycobacterium tuberculosis with vaccine potential. Vaccine 23: 1265-1272.
• Ramakrishnan L, Federspiel NA, Falkow S (2000) Granuloma-specific expression of Mycobacterium virulence proteins from the glycine-rich PE-PGRS family. Science 288: 1436-1439.
• Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38: D46-D51.
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
• Zhang Y, Chen C, Liu J, Deng H, Pan A, Zhang L, Zhao X, Huang M, Lu B, Dong H, Du P, Chen W, Wan K (2011) Complete genome sequences of Mycobacterium tuberculosis strains CCDC5079 and CCDC5080, which belong to the Beijing family. J Bacteriol 193: 5591-5592.
• Friedman CR, Stoeckle MY, Johnson WD Jr, Riley LW (1995) Double-repetitive-element PCR method for subtyping Mycobacterium tuberculosis clinical isolates. J Clin Microbiol 33: 1383-1384.
• Kotlowski R, Shamputa IC, El Aila NA, Sajduda A, Rigouts L, van Deun A, Portaels F (2004) PCR-based genotyping of Mycobacterium tuberculosis with new GC-rich repeated sequences and IS6110 inverted repeats used as primers. J Clin Microbiol 42: 372-377.
• Goulding JN, Stanley J, Saunders N, Arnold C (2000) Genome-sequence-based fluorescent amplified-fragment length polymorphism analysis of Mycobacterium tuberculosis. J Clin Microbiol 38: 1121-1126.
• Kremer K, van Soolingen D, Frothingham R, Haas WH, Hermans PW, Martín C, Palittapongarnpim P, Plikaytis BB, Riley LW, Yakrus MA, Musser JM, van Embden JD (1999) 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.

Identifiers

DOI

10.18388/abp.2015_1037