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The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen

Abstract

The results of detection and identification of Bacillus anthracis strains in loop-mediated isothermal DNA amplification (LAMP) reaction performed under optimized conditions with original primers and thermostable DNA polymerase are presented. Reproducible LAMP-based detection of chromosomal and plasmid DNA targets specific for B. anthracis strains has been demonstrated. No cross reactions with DNA from bacterial strains of other species of the B. cereus group were detected. The development of tests for anthrax-pathogen detection based on the optimized reaction of loop isothermal DNA amplification is planned. These tests will be convenient for clinical studies and field diagnostics due to the absence of requirements for sophisticated equipment.

References

  1. 1.

    Daffonchio, D., Cherif, A., Brusetti, L., Rizzi, A., Mora, D., Boudabous, A., et al., Nature of polymorphisms in 16S–23S rRNA gene intergenic transcribed spacer fingerprinting of bacillus and related genera, Appl. Environ. Microbiol., 2003, vol. 69, pp. 5128–5137.

  2. 2.

    Priest, F., Barker, M., Baillie, L., Holmes, E., and Maiden, M., Population structure and evolution of the Bacillus cereus group, J. Bacteriol., 2004, vol. 186, pp. 7959–7970.

  3. 3.

    Van Ert, M., Easterday, W., Huynh, L., Okinaka, R., Hugh-Jones, M., Ravel, J., et al., Global genetic population structure of Bacillus anthracis, PloS One, 2007, vol. 2, p. e461.

  4. 4.

    Van Ert, M., Easterday, W., Simonson, T., U’Ren, J., Pearson, T., Kenefic, L., et al. Strain-specific singlenucleotide polymorphism assays for the Bacillus anthracis Ames strain, J. Clin. Microbiol., 2007, vol. 45, pp. 47–53.

  5. 5.

    Luna, V., King, D., Peak, K., Reeves, F., Heberlein-Larson, L., and Veguilla, W., Bacillus anthracis virulent plasmid pX02 genes found in large plasmids of two other Bacillus species, J. Clin. Microbiol., 2006, vol. 44, no. 7, pp. 2367–2377.

  6. 6.

    Han, C., Xie, G., Challacombe, J., Altherr, M., Bhotika, S., Brown, N., et al., Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis, J. Bacteriol., 2006, vol. 188, pp. 3382–3390.

  7. 7.

    Hoffinaster, A., Ravel, J., Rasko, D., Chapman, G., Chute, M., Marston, C., et al., Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax, Proc. Natl. Acad. Sci. U. S. A., 2004, vol. 101, no. 22, pp. 8449–8454.

  8. 8.

    Hoffinaster, A., Hill, K., Gee, J., Marston, C., De, B., Popovic, T., et al., Characterization of Bacillus cereus isolates associated with fatal pneumonias: Strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes, J. Clin. Microbiol., 2006, vol. 44, no. 9, pp. 3352–3360.

  9. 9.

    Hoffinaster, A., Novak, R., Marston, C., Gee, J., Helsel, L., Pruckler, J., and Wilkins, P., Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing, BMC Microbiol., 2008, vol. 8, p. 191.

  10. 10.

    Oh, S.Y., Budzik, J.M., Garufi, G., and Schneewind, O., Two capsular polysaccharides enable Bacillus cereus G9241 to cause anthraxlike disease, Mol. Microbiol., 2011, vol. 80, pp. 455–470.

  11. 11.

    Klee, S., Brzuszkiewicz, E., Nattermann, H., Bruggemann, H., Dupke, S., Wollherr, A., et al., The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids, PloS One, 2010, vol. 5, p. e10986.

  12. 12.

    Hu, X., Van der Auwera, G., Timmery, S., Zhu, L., and Mahillon, J., Distribution, diversity, and potential mobility of extrachromosomal elements related to the Bacillus anthracis pXO1 and pXO2 virulence plasmids, Appl. Environ. Microbiol., 2009, vol. 75, pp. 3016–3028.

  13. 13.

    Van der Auwera, G., Andrup, L., and Mahillon, J., Conjugative plasmid pAw63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727, BMC Genomics, 2005, vol. 6, p. 103.

  14. 14.

    Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., and Hase, T., Loop-mediated isothermal amplification of DNA, Nucleic Acids Res., 2000, vol. 28, no. 12, p. E63.

  15. 15.

    Notomi, T., Kanda, H., Taguch, F., Minekaw, H., Itamura, S., Odagiri, T, and Tashiro, M., RT-LAMP method provides a simple, rapid and specific detection system for SARS-CoV RNA, Proc. Int. Conference on SARS, Lübeck: German Medical Science, 2004.

  16. 16.

    Parida, M., Sannarangaiah, S., Dash, P.K., Rao, P.V.L., and Morita, K., Loop mediated isothermal amplification (LAMP): A new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases, Rev. Med. Virol., 2008, vol. 18, pp. 407–421.

  17. 17.

    Pandey, B.D., Poudel, A., Yoda, T., Tamaru, A., Oda, N., Fukushima, Y., et al., Development of an in-house loop-mediated isothermal amplification (LAMP) assay for detection of Mycobacterium tuberculosis and evaluation in sputum samples of Nepalese patients, J. Med. Microbiol., 2008, vol. 57, pp. 439–443.

  18. 18.

    Geojith, G., Dhanasekaran, S., Chandran, S.P., and Kenneth, J., Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting, J. Microbiol. Methods, 2011, vol. 84, pp. 71–73.

  19. 19.

    Sonthayanon, P., Chierakul, W., Wuthiekanun, V., Thaipadungpanit, J., Kalambaheti, T., Boonsilp, S., et al., Accuracy of loop-mediated isothermal amplification for diagnosis of human leptospirosis in Thailand, Am. J. Trop. Med. Hyg., 2011, vol. 84, pp. 614–620.

  20. 20.

    Lim, K.T., Teh, C.S.J., and Thong, K.L., Loop mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus, Bio. Med. Res. Int., 2013, vol. 2013, p. 895816.

  21. 21.

    Tang, M.J., Zhou, S., Zhang, X.Y., Pu, J.H., Ge, Q.L., Tang, X.J., and Gao, Y.S., Rapid and sensitive detection of Listeria monocytogenes by loop-mediated isothermal amplification, Curr. Microbiol., 2011, vol. 63, pp. 511–516.

  22. 22.

    Yamazaki, W., Seto, K., Taguchi, M., Ishibashi, M., and Inoue, K., Sensitive and rapid detection of cholera toxin producing Vibrio cholerae using a loop mediated isothermal amplification, BMC Microbiol., 2008, vol. 8, p. 94.

  23. 23.

    Kawai, Y., Kimura, Y., Lezhava, A., Kanamori, H., Usui, K., Hanami, T., et al., One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RTSmartAmp Assay and its clinical validation, PloS One, 2012, vol. 7, no. 1, p. e30236.

  24. 24.

    Moslemi, E., Shahhosseiny, M.H., Javadi, G., Praivar, K., Sattari, T.N., and Amini, H.K., Loop mediated isothermal amplification (LAMP) for rapid detection of HBV in Iran, Afr. J. Microbiol. Res., 2009, vol. 3, pp. 439–445.

  25. 25.

    Qiao, Y.-M., Guo, Y.-C., Zhang, X.-En., Zhou, Y.-F., Zhang, Z.-P., Wei, H.-P., et al., Loop-mediated isothermal amplification for rapid detection of Bacillus anthracis spores, Biotechnol. Lett., 2007, vol. 29, pp. 1939–1946.

  26. 26.

    Hatano, B., Maki, T., Obara, T., Fukumoto, H., Hagisawa, K., Matsushita, Y., et al., LAMP using a disposable pocket warmer for anthrax detection, a highly mobile and reliable method for anti-bioterrorism, Jpn. J. Infect. Dis., 2010, vol. 63, pp. 36–40.

  27. 27.

    Dugan, L., Bearinger, J., Hinckley, A., Strout, C., and Souza, B., Detection of Bacillus anthracis from spores and cells by loop-mediated isothermal amplification without sample preparation, J. Microbiol. Methods, 2012, vol. 90, no. 3, pp. 280–284.

  28. 28.

    Jain, N., Kumar, J.S., Parida, M.M., Merwyn, S., Rai, G.P., and Agarwal, G.S., Real-time loop-mediated isothermal amplification assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder, J. Microbiol. Biotechnol., 2011, vol. 27, no. 6, pp. 1407–1413.

  29. 29.

    Kurosaki, Y., Sakuma, T., Fukuma, A., Fujinami, Y., Kawamoto, K., Kamo, N., et al., A simple and sensitive method for detection of Bacillus anthracis by loopmediated isothermal amplification, J. Appl. Microbiol., 2009, vol. 107, no. 6, pp. 1947–1956.

  30. 30.

    Radnedge, L., Agron, P.G., Hill, K.K., Jackson, P.J., Ticknor, L.O., Keim, P., and Andersen, G.L., Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis, Appl. Environ. Microbiol., 2003, vol. 69, no. 5, pp. 2755–2764.

  31. 31.

    Nagamine, K., Watanabe, K., Ohtsuka, K., Hase, T., and Notomi, T., Loop-mediated isothermal amplification reaction using a nondenatured template, Clin. Chem., 2001, vol. 47, pp. 1742–1743.

  32. 32.

    Wozniakowski, G., Kozdrun, W., and Samorek-Salamonowicz, E., Loop-mediated isothermal amplification for the detection of goose circovirus, Virol. J., 2012, vol. 9, p. 110.

  33. 33.

    Ignatov, K.B., Barsova, E.V., Fradkov, A.F., Blagodatskich, K.A., Kramarova, T.V., and Kramarov, V.M., A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification, BioTechniques, 2014, vol. 57, pp. 81–87.

  34. 34.

    Shishkova, N.A., Mokrievich, A.N., Pavlov, V.M., Marinin, L.I., Vakhrameeva, G.M., Kudryavtseva, T.Yu., and Dyatlov, I.A., Usage of chi-sequence for differentiating the strains of anthrax from closely related bacilli, Probl. Osobo Opasnykh Infekts., 2014, no. 1, pp. 97–100.

  35. 35.

    Shishkova, N.A., Mokrievich, A.N., Platonov, M.E., Svetoch, T.E., and Marinin, L.I., The way for studying genetic diversity of anthrax strains from the collection of State Research Center for Applied Microbiology and Biotechnology, Probl. Osobo Opasnykh Infekts., 2010, vol. 2, no. 104, pp. 60–66.

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Author information

Correspondence to A. N. Mokrievich.

Additional information

Original Russian Text © I.Yu. Shchit, K.B. Ignatov, T.Yu. Kudryavtseva, N.A. Shishkova, R.I. Mironova, L.I. Marinin, A.N. Mokrievich, V.M. Kramarov, S.F. Biketov, I.A. Dyatlov, 2017, published in Molekulyarnaya Genetika, Mikrobiologiya i Virusologiya, 2017, No. 2, pp. 69–76.

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Shchit, I.Y., Ignatov, K.B., Kudryavtseva, T.Y. et al. The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen. Mol. Genet. Microbiol. Virol. 32, 100–108 (2017). https://doi.org/10.3103/S0891416817020094

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Keywords

  • loop isothermal amplification of DNA
  • LAMP
  • Bacillus anthracis