Skip to main content
SpringerLink
Log in

Comparative Analysis of Genotyping Methods for Bacillus anthracis

  • GENETICS OF MICROORGANISMS
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Genetic typing of the anthrax causative agent is used in epidemiological investigations of infection outbreaks and serves as a tool for studying the evolution of this pathogenic species. Analytical, technical, and economic possibilities of the most common modern methods of genetic typing of B. anthracis have been studied on the basis of our own and published data. It was established that canSNP genotyping distinguishes 10 genotypes among 23 strains of B. anthracis with a diversity index DI of 0.8261. DI for MLST is no more than 0.5495–0.5790, depending on the sample of strains. DI for MLVA15, 25, and 31 is the same and equal to 0.9881. SNP analysis of the core region of genomes of 181 strains provides the highest discrimination (DI = 1). MVLST with a DI of 0.9960, like SNR analysis, reveals differences between genotypes of isolates from the same outbreak. CanSNP13 genotyping is quite sufficient as a preliminary stage of genotyping for the separation of strains into the main genetic lines. MLST of B. anthracis is impractical owing to low resolution and laboriousness, and MVLST, despite its high resolution, is impractical owing to the length and laboriousness of the study. The identity of isolates from the same anthrax outbreak can be confirmed using MLVA15–31; the subtle differences between them are the methods of SNR and SNP analysis of the core region of the genome.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.

Similar content being viewed by others

REFERENCES

  1. Andersen, G.L., Simchock, J.M., and Wilson, K.H., Identification of a region of genetic variability among Bacillus anthracis strains and related species, J. Bacteriol., 1996, vol. 178, no. 2, pp. 377—384.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Keim, P., Price, L.B., Klevytska, A.M., et al., Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis, J. Bacteriol., 2000, vol. 182, no. 10, pp. 2928—2936.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Le Flèche, P., Hauck, Y., Onteniente, L., et al., A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis, BMC Microbiol., 2001, vol. 1, no. 2. http://www.biomedcentral.com/1471-2180/1/2.

  4. Lista, F., Faggioni, G., Valjevac, S., et al., Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis, BMC Microbiol., 2006, vol. 6, no. 33, pp. 1—14. https://doi.org/10.1186/1471-2180-6-33

    Article  CAS  Google Scholar 

  5. Beyer, W., Bellan, S., Eberle, G., et al., Distribution and molecular evolution of Bacillus anthracis genotypes in Namibia, PLoS Negl. Trop. Dis., 2012, vol. 6, no. 3. pp. 1—12.

    Article  CAS  Google Scholar 

  6. Thierry, S. Tourterel, C., Le Fleche, P., et al., Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database, PLoS One, 2014, vol. 9, no. 6. 95131. https://doi.org/10.1371/journal.pone.0095131

    Article  CAS  Google Scholar 

  7. Hoffmaster, A.R., Fitzgerald, C.C., Ribot, E., et al., Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, united states, Emerging Infect. Dis., 2002, vol. 8, no. 10, pp. 1111—1116.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Fouet, A., Smith, K.L., Keys, C., et al., Diversity among french Bacillus anthracis Isolates, J. Clin. Microbiol., 2002, vol. 40, no. 12, pp. 4732—4734.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Tsygankova, O.I., Eremenko, E.I., Bryukhanov, A.F., et al., Genotyping of Bacillus anthracis strains in the CIS region// Zh. Mikrobiol., 2003, no. 6, suppl., pp. 51—56.

  10. Gierczyński, R., Kałuzewski, S., Rakin, A., et al., Intriguing diversity of Bacillus anthracis in eastern Poland—the molecular echoes of the past outbreaks, FEMS Microbiol. Lett., 2004, vol. 239, pp. 235—240.

    Article  CAS  PubMed  Google Scholar 

  11. Fasanella, A., Van Ert, M., Altamura, S.A., et al., Molecular diversity of Bacillus anthracis in Italy, J. Clin. Microbiol., 2005, vol. 43, no. 7, pp. 3398—3401.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ryu, C., Lee, K., Hawng, H.-J., et al., Molecular characterization of Korean Bacillus anthracis isolates by amplified fragment length polymorphism analysis and multilocus variable-number tandem repeat analysis, Appl. Environ. Microbiol., 2005, vol. 71, no. 8, pp. 4664—4671.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Merabishvili, M., Natidze, M., Rigvava, S., et al., Diversity of Bacillus anthracis strains in Georgia and of vaccine strains from the former Soviet Union, Appl. Environ. Microbiol., 2006, vol. 72, no. 8, pp. 5631—5636.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Sue, D., Marston, C.K., Hoffmaster, A.R., et al., Genetic diversity in a Bacillus anthracis historical collection (1954 to 1988), J. Clin. Microbiol., 2007, vol. 45, no. 6, pp. 1777—1782.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shishkova, N.A., Mokrievich, A.N., Platonov, M.E., et al., The study of the genetic diversity of Bacillus anthracis strains from the collection of FBIS SRCAMB, Probl. Osobo Opasnykh Infekts., 2010, no. 104, pp. 60—65.

  16. Aikembayev, A.M., Lukhnova, L., Temiraliyeva, G., et al., Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan, Emerging Infect. Dis., 2010, vol. 16, no. 5, pp. 789—796.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Okutani, A., Tungalag, H., Boldbaatar, B., et al., Molecular epidemiological study of Bacillus anthracis isolated in Mongolia by multiple-locus variable-number tandem repeat analysis for 8 loci (MLVA-8), Jpn. J. Infect. Dis., 2011, vol. 64, pp. 345—348.

    PubMed  Google Scholar 

  18. Pilo, P. and Frey, J., Bacillus anthracis: Molecular taxonomy, population genetics, phylogeny and patho-evolution, Infect. Genet. Evol., 2011, vol. 11, no. 6, pp. 1218—1224. https://doi.org/10.1016/j.meegid.2011.05.013

    Article  CAS  PubMed  Google Scholar 

  19. Eremenko, E.I., Ryazanova, A.G., Tsygankova, O.I., et al., Genotype diversity of Bacillus anthracis strains isolated from the Caucasus region, Mol. Genet., Microbiol. Virol., 2012, vol. 27, no. 2, pp. 74—78. https://doi.org/10.3103/S0891416812020024.

    Article  Google Scholar 

  20. Afanas’ev, M.V., Kravets, E.V., Dugarzhapova, Z.F., et al., Comparative multilocus VNTR and SNP analysis of Bacillus anthracis vaccine strains, Mol. Genet., Microbiol. Virol., 2014, no. 2. pp. 86—92. https://doi.org/10.3103/S0891416814020025.

  21. Timofeev, V.S., Bakhteeva, I.V., and Dyatlov, I.A., Genotyping of Bacillus anthracis and closely related microorganisms, Russ. J. Genet., 2018, vol. 54, no. 1. pp. 1—11. https://doi.org/10.1134/S1022795418010118.

    Article  CAS  Google Scholar 

  22. Keim, P., Van Ert, M.N., and Pearson, T., Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales, Infect., Gen. Evol., 2004, no. 4, pp. 205—213.

  23. Stratilo, C.W., Lewis, C.T., Bryden, L., et al., Single-nucleotide repeat analysis for subtyping Bacillus anthracis isolates, J. Clin. Microbiol., 2006, vol. 44, no. 3, pp. 777—782. https://doi.org/10.1128/JCM.44.3.777-782.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kenefic, L.J., Beaudry, J., Trim, C., et al., A high resolution four-locus multiplex single nucleotide repeat (SNR) genotyping in Bacillus anthracis, J. Microbiol. Methods, 2008, vol. 73, no. 3, pp. 269—272. https://doi.org/10.1016/j.mimet.2007.11.014

    Article  CAS  PubMed  Google Scholar 

  25. Kenefic, L.J., Beaudry, J., Trim, C., et al., High resolution genotyping of Bacillus anthracis outbreak strains using four highly mutable single nucleotide repeat markers, Lett. Appl. Microbiol., 2008, vol. 46, no. 5, pp. 600—603. https://doi.org/10.1111/j.1472-765X.2008.02353.x

    Article  CAS  PubMed  Google Scholar 

  26. Stratilo, C.W. and Bader, D.E., Genetic diversity among Bacillus anthracis soil isolates at fine geographic scales, Appl. Environ. Microbiol., 2012, vol. 78, no. 18, pp. 6433—6437.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Garofolo, G., Ciammaruconi, A., Fasanella, A., et al., SNR analysis: molecular investigation of an anthrax epidemic, BMC Veter. Res., 2010. 6:11. http://www. biomedcentral.com/1746-6148/6/11.

  28. Van Ert, M.N., Easterday, W.R., Huynh, L.Y., et al., Global genetic population structure of Bacillus anthracis, PLoS One, 2007, vol. 2, no. 5, pp. 1—10. e461. https://doi.org/10.1371/journal.pone.0000461

  29. Girault, G., Thierry, S., Cherchame, E., and Derzelle, S., Application of high-throughput sequencing: discovery of informative SNPs to subtype Bacillus anthracis, Adv. Biosci. Biotech., 2014, no. 5, pp. 669—677. https://doi.org/10.4236/abb.2014.57079.

  30. Yamashita, A., Sekizuka, T., and Kuroda, M., GcoGSA-BA: a global core genome SNP analysis for Bacillus anthracis, Health Secur., 2015, vol. 13, no. 1, pp. 64—68. https://doi.org/10.1089/hs.2014.0076

    Article  PubMed  PubMed Central  Google Scholar 

  31. Leekitcharoenphon, P., Kaas, R.S., Thomsen, M.C., et al., SnpTree—a web-server to identify and construct SNP trees from whole genome sequence data, BMC Genomics, 2012, vol. 13, suppl. 7:S6.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Keim, P., Grunowc, R., Vipond, R., et al., Whole genome analysis of injectional anthrax identifies two disease clusters spanning more than 13 years, EBioMedicine, 2015, vol. 2, no. 6, pp. 1613—1618. . eCollection 2015. https://doi.org/10.1016/j.ebiom.2015.10.004

  33. Derzelle, S., Aguilar-Bulteta, L., and Freya, J., Whole genome SNP analysis of bovine B. anthracis strains from Switzerland reflects strict regional separation of Simmental and Swiss brown breeds in the past, Vet. Microbiol., 2016, vol. 196, pp. 1—8. http://dx.org/10.1016/j.vetmic.2016.10.014.

    Article  PubMed  Google Scholar 

  34. Antwerpen, M.H., Sahl, J.W., Birdsell, D., et al., Unexpected relations of historical anthrax strain, mBio, 2017. 8:e00440-17. https://org/ https://doi.org/10.1128/mBio.00440-17

  35. Derzelle, S., Girault, G., Roest, H.I., et al., Molecular diversity of Bacillus anthracis in the Netherlands: investigating the relationship to the worldwide population using whole-genome SNP discovery, Infect., Gen. Evol., 2015, vol. 32, pp. 370—376. http://dx.org/10.1016/j.meegid.2015.03.030.

    Google Scholar 

  36. Sabat, A.J., Budimir, A., Nashev, D., et al., Overview of molecular typing methods for outbreak detection and epidemiological surveillance, Euro Surveill., 2013, vol. 18, no. 4, pp. 1—14. pii=20380. http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=2038.

  37. Kulichenko, A.N., Eremenko, E.I., Ryazanova, A.G., et al., Biological properties and molecular genetic characterization of Bacillus anthracis strains isolated during the anthrax outbreak in the Yamalo-Nenets Autonomous Okrug in 2016, Probl. Osobo Opasnykh Infekts., 2017, no. 1. pp. 94—99. https://doi.org/10.21055/0370-1069-2017-1-94-99

  38. Opyt likvidatsii vspyshki sibirskoi yazvy na Yamale v 2016 (The Experience of Eliminating the Outbreak of Anthrax on Yamal in 2016), Popova, A.Yu. and Kulichenko, A.N., Eds., Izhevsk: Print 2, 2017.

  39. Koteneva, E.A., Tsygankova, O.I., and Eremenko, E.I. Analysis of canSNP genotypes of Bacillus anthracis strains isolated on the territory of the Northern Caucasus and Transcaucasia, Aktual’nye problemy epidemiologii i profilakticheskoi meditsiny (Current Issues in Epidemiology and Preventive Medicine) (Proc. 6th All-Russ. Theor. Prakt. Conf. of Young Scientists and Specialists of Federal Service for Supervision of Consumer Rights Protection and Human Welfare), Stavropol, 2014.

  40. Hunter, P.R. and Gaston, M.A., Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity, J. Clin Microbiol., 1988, vol. 26, no. 11, pp. 2465—2466.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Okinaka, R.T., Henrie, M., Hill, K.K., et al., Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue, Emerging Infect. Dis., 2008, vol. 14, no. 4, pp. 653—656. https://doi.org/10.3201/eid1404.070984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ågren, J., Finn, M., Bengtsson, B., and Segerman, B., Microevolution during an anthrax outbreak leading to clonal heterogeneity and penicillin resistance, PLoS One, 2014, vol. 9, no. 2, pp. 1—14. e89112. https://doi.org/10.1371/journal.pone.0089112

  43. Eremenko, E.I., Ryazanova, A.G., Tsygankova, E.A., et al., Genotypic features of Bacillus anthracis strains with different manifestations of pathogenicity related traits, Probl. Osobo Opasnykh Infekts., 2010, no. 104. pp. 53—56.

Download references

Author information

Authors and Affiliations

  1. Stavropol Plague Control Research Institute, 355035, Stavropol, Russia

    E. I. Eremenko, A. G. Ryazanova, S. V. Pisarenko, L. Yu. Aksenova, O. V. Semenova, E. A. Koteneva, O. I. Tsygankova, D. A. Kovalev, T. M. Golovinskaya, D. K. Chmerenko & A. N. Kulichenko

Authors
  1. E. I. Eremenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. G. Ryazanova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. V. Pisarenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. Yu. Aksenova
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. O. V. Semenova
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. E. A. Koteneva
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. O. I. Tsygankova
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. D. A. Kovalev
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. T. M. Golovinskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. D. K. Chmerenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. A. N. Kulichenko
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to E. I. Eremenko.

Additional information

Translated by A. Ostyak

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Eremenko, E.I., Ryazanova, A.G., Pisarenko, S.V. et al. Comparative Analysis of Genotyping Methods for Bacillus anthracis. Russ J Genet 55, 35–44 (2019). https://doi.org/10.1134/S102279541901006X

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S102279541901006X

Keywords:

Search

Navigation