跳至主要内容

Application of High-Throughput Sequencing: Discovery of Informative SNPs to Subtype Bacillus anthracis

Read full paper at:
http://www.scirp.org/journal/PaperInformation.aspx?PaperID=47443#.VFnEDWfHRK0

Single Nucleotide Polymorphisms (SNPs) are the most common and abundant genetic variation found in the genome of any living species, from bacteria to humans. In bacterial genotyping, these evolutionarily stable point mutations represent important DNA markers that can be used to elucidate deep phylogenetic relationships among worldwide strains, but also to discriminate closely related strains. With the advent of next generation sequencing (NGS) technologies, affordable solutions are now available to get access to the complete genome sequence of an organism. Sequencing efforts of an increasing number of strains provide an unprecedented opportunity to create comprehensive species phylogenies. In this study, a comparative analysis of 161 genomes of Bacillus anthracis has being conducted to discover new informative SNPs that further resolves B. anthracis SNP-based phylogenetic tree. Nine previously unpublished SNPs that define major groups or sub-groups within the B. anthracis species were selected and developed into SNP discriminative assays. We report here a cost-effective high-resolution melting-based genotyping method for the screening of 27 canonical SNPs that includes these new diagnostic markers. The present assays are useful to rapidly assign an isolate to one sub-lineages or sub-groups and determine its phylogenetic placement on the B. anthracis substructure population.
Cite this paper
Girault, G. , Thierry, S. , Cherchame, E. and Derzelle, S. (2014) Application of High-Throughput Sequencing: Discovery of Informative SNPs to Subtype Bacillus anthracis. Advances in Bioscience and Biotechnology, 5, 669-677. doi: 10.4236/abb.2014.57079.
 

[1] Keim, P., Okinaka, R. and Pearson, T. (2013) The Evolution and Global Dissemination of Bacillus anthracis. The International Conference on Bacillus anthracis, B. cereus, and B. thuringiensis, Victoria, 1-5 September 2013.
[2] Rasko, D.A., Worsham, P.L., Abshire, T.G., Stanley, S.T., Bannan, J.D., Wilson, M.R., Langham, R.J., Decker, R.S., Jiang, L., Read, T.D., et al. (2011) Bacillus anthracis Comparative Genome Analysis in Support of the Amerithrax Investigation. Proceedings of the National Academy of Sciences of the United States of America, 108, 5027-5032.
http://dx.doi.org/10.1073/pnas.1016657108
[3] Keim, P., Price, L.B., Klevytska, A.M., Smith, K.L., Shupp, J.M., Okinaka, R., Jackson, P.J. and Hugh-Jones, M.E. (2000) Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis. Journal of Bacteriology, 182, 2928-2936.
http://dx.doi.org/10.1128/JB.182.10.2928-2936.2000
[4] Lista, F., Faggioni, G., Valjevac, S., Ciammaruconi, A., Vaissaire, J., le Doujet, C., Gorge, O., De Santis, R., Carattoli, A., Ciervo, A., et al. (2006) Genotyping of Bacillus anthracis Strains Based on Automated Capillary 25-Loci Multiple Locus Variable-Number Tandem Repeats Analysis. BMC Microbiology, 6, 1-15.
[5] Le Flèche, P., Hauck, Y., Onteniente, L., Prieur, A., Denoeud, F., Ramisse, V., Sylvestre, P., Benson, G., Ramisse, F. and Vergnaud, G. (2001) A Tandem Repeats Database for Bacterial Genomes: Application to the Genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiology, 1, 2.
[6] Stratilo, C.W., Lewis, C.T., Bryden, L., Mulvey, M.R. and Bader, D. (2006) Single-Nucleotide Repeat Analysis for Subtyping Bacillus anthracis Isolates. Journal of Clinical Microbiology, 44, 777-782.
http://dx.doi.org/10.1128/JCM.44.3.777-782.2006
[7] Kenefic, L.J., Beaudry, J., Trim, C., Daly, R., Parmar, R., Zanecki, S., Huynh, L., Van Ert, M.N., Wagner, D.M., Graham, T., et al. (2008) High Resolution Genotyping of Bacillus anthracis Outbreak Strains Using Four Highly Mutable Single Nucleotide Repeat Markers. Letters in Applied Microbiology, 46, 600-603.
http://dx.doi.org/10.1111/j.1472-765X.2008.02353.x
[8] Garofolo, G., Ciammaruconi, A., Fasanella, A., Scasciamacchia, S., Adone, R., Pittiglio, V. and Lista, F. (2010) SNR Analysis: Molecular Investigation of an Anthrax Epidemic. BMC Veterinary Research, 6, 11.
http://dx.doi.org/10.1186/1746-6148-6-11
[9] Keim, P., Van Ert, M.N., Pearson, T., Vogler, A.J., Huynh, L.Y. and Wagner, D.M. (2004) Anthrax Molecular Epidemiology and Forensics: Using the Appropriate Marker for Different Evolutionary Scales. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 4, 205-213.
[10] Van Ert, M.N., Easterday, W.R., Huynh, L.Y., Okinaka, R.T., Hugh-Jones, M.E., Ravel, J., Zanecki, S.R., Pearson, T., Simonson, T.S., U’Ren, J.M., et al. (2007) Global Genetic Population Structure of Bacillus anthracis. PLoS One, 2, Article ID: e461.
[11] Kuroda, M., Serizawa, M., Okutani, A., Sekizuka, T., Banno, S. and Inoue, S. (2010) Genome-Wide Single Nucleotide Polymorphism Typing Method for Identification of Bacillus anthracis Species and Strains among B. cereus Group Species. Journal of Clinical Microbiology, 48, 2821-2829.
http://dx.doi.org/10.1128/JCM.00137-10
[12] Marston, C.K., Allen, C.A., Beaudry, J., Price, E.P., Wolken, S.R., Pearson, T., Keim, P. and Hoffmaster, A.R. (2011) Molecular Epidemiology of Anthrax Cases Associated with Recreational Use of Animal Hides and Yarn in the United States. PLos One, 6, Article ID: e28274.
http://dx.doi.org/10.1371/journal.pone.0028274
[13] Price, E.P., Seymour, M.L., Sarovich, D.S., Latham, J., Wolken, S.R., Mason, J., Vincent, G., Drees, K.P., Beckstrom-Sternberg, S.M., Phillippy, A.M., et al. (2012) Molecular Epidemiologic Investigation of an Anthrax Outbreak among Heroin Users, Europe. Emerging Infectious Diseases, 18, 1307-1313.
http://dx.doi.org/10.3201/eid1808.111343
[14] Vogler, A.J., Busch, J.D., Percy-Fine, S., Tipton-Hunton, C., Smith, K.L. and Keim, P. (2012) Molecular Analysis of Rifampicin Resistance in Bacillus anthracis and Bacillus cereus. Antimicrobial Agents and Chemotherapy, 46, 511-513.
http://dx.doi.org/10.1128/AAC.46.2.511-513.2002
[15] Keim, P., Kalif, A., Shupp, J., Hill, K., Travis, S.E., Richmond, K., Adair, D.M., Hugh-Jones, M., Kuske, C.R. and Jackson, P. (1997) Molecular Evolution and Diversity in Bacillus anthracis as Detected by Amplified Fragment Length Polymorphism Markers. Journal of Bacteriology, 179, 818-824.
[16] Keim, P., Gruendike, J.M., Klevytska, A.M., Schupp, J.M., Challacombe, J. and Okinaka, R. (2009) The Genome and Variation of Bacillus anthracis. Molecular Aspects of Medicine, 30, 397-405.
http://dx.doi.org/10.1016/j.mam.2009.08.005
[17] Smith, K.L., DeVos, V., Bryden, H., Price, L.B., Hugh-Jones, M.E. and Keim, P. (2000) Bacillus anthracis Diversity in Kruger National Park. Journal of Clinical Microbiology, 38, 3780-3784.
[18] Derzelle, S., Laroche, S., Le Fleche, P., Hauck, Y., Thierry, S., Vergnaud, G. and Madani, N. (2011) Characterization of Genetic Diversity of Bacillus anthracis in France by Using High-Resolution Melting Assays and Multilocus Variable-Number Tandem-Repeat Analysis. Journal of Clinical Microbiology, 49, 4286-4292.
http://dx.doi.org/10.1128/JCM.05439-11
[19] Garofolo, G., Serrecchia, L., Corro, M. and Fasanella, A. (2011) Anthrax Phylogenetic Structure in Northern Italy. BMC Research Notes, 4, 273.
http://dx.doi.org/10.1186/1756-0500-4-273
[20] Pilo, P., Perreten, V. and Frey, J. (2008) Molecular Epidemiology of Bacillus anthracis: Determining the Correct Origin. Applied and Environmental Microbiology, 74, 2928-2931.
http://dx.doi.org/10.1128/AEM.02574-07
[21] Gierczyński, R., Kaluzewski, S., Rakin, A., Jagielski, M., Zasada, A., Jakubczak, A., Borkowska-Opacka, B. and Rastawicki, W. (2004) Intriguing Diversity of Bacillus anthracis in Eastern Poland—The Molecular Echoes of the Past Outbreaks. FEMS Microbiology Letters, 239, 235-240.
[22] Sue, D., Marston, C.K., Hoffmaster, A.R. and Wilkins, P.P. (2007) Genetic Diversity in a Bacillus anthracis Historical Collection (1954 to 1988). Journal of Clinical Microbiology, 45, 1777-1782.
[23] Derzelle, S. and Thierry, S. (2013) Genetic Diversity of Bacillus anthracis in Europe: Genotyping Methods in Forensic and Epidemiologic Investigations. Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science, 11, S166-S176.
[24] Girault, G., Blouin, Y., Vergnaud, G. and Derzelle, S. (2014) High-Throughput Sequencing of Bacillus anthracis in France: Investigating Genome Diversity and Population Structure Using Whole-Genome SNP Discovery. BMC Genomics, 15, 288.
[25] NCBI. http://www.ncbi.nlm.nih.gov/
[26] Erali, M., Voelkerding, K.V. and Wittwer, C.T. (2008) High Resolution Melting Applications for Clinical Laboratory Medicine. Experimental and Molecular Pathology, 85, 50-58.
[27] Hurtle, W., Bode, E., Kulesh, D.A., Kaplan, R.S., Garrison, J., Bridge, D., House, M., Frye, M.S., Loveless, B. and Nordwood, D. (2004) Detection of the Bacillus anthracis gyrA Gene by Using a Minor Groove Binder Probe. Journal of Clinical Microbiology, 42, 179-185.
[28] Easterday, W.R., Van Ert, M.N., Zanecki, S. and Keim, P. (2005) Specific Detection of Bacillus anthracis Using a TaqMan Mismatch Amplification Mutation Assay. Biotechniques, 38, 731-735.
[29] Birdsell, D.N., Pearson, T., Price, E.P., Hornstra, H.M., Nera, R.D., Stone, N., Gruendike, J., Kaufman, E.L., Pettus, A.H., Hurbon, A.N., et al. (2012) Melt Analysis of Mismatch Amplification Mutation Assays (Melt-MAMA): A Functional Study of a Cost-Effective SNP Genotyping Assay in Bacterial Models. PLoS One, 7, Article ID: e32866.
[30] Kenefic, L.J., Pearson, T., Okinaka, R.T., Schupp, J.M., Wagner, D.M., Hoffmaster, A.R., Trim, C.B., Chung, W.K., Beaudry, J.A., Jiang, L., et al. (2009) Pre-Columbian Origins for North American Anthrax. PLoS One, 4, Article ID: e4813.
[31] Simonson, T.S., Okinaka, R.T., Wang, B., Easterday, W.R., Huynh, L., U’Ren, J.M., Dukerich, M., Zanecki, S.R., Kenefic, L.J., Beaudry, J., et al. (2009) Bacillus anthracis in China and Its Relationship to Worldwide Lineages. BMC Microbiology, 9, 71.
[32] Okinaka, R.T., Henrie, M., Hill, K.K., Lowery, K.S., Van Ert, M., Pearson, T., Shupp, J., Kenefic, L., Beaudry, J., Hofstadler, S.A., et al. (2008) Single Nucleotide Polymorphism Typing of Bacillus anthracis from Sverdlovsk Tissue. Emerging Infectious Diseases, 14, 653-656.        eww141105lx
标签：

评论

发表评论

此博客中的热门博文

Does Immigration Promote the Investment of the Monopolistic Firm?

In the present paper, we examine the effect of increasing uncertainty of immigrants’ growth on the optimal timing of investment of a firm that has a monopolistic power over the labor market. It is revealed that when the uncertainty of immigrants’ growth is more than a threshold level, increasing uncertainty of immigrants’ growth accelerates the optimal timing of firms’ investment and enhances the economic growth, even if the uncertainty of immigrants’ growth is formulated by the geometric Brownian motion, which is in sharp contrast to the standard result that an increase in the uncertainty postpones the optimal timing. With an increase in the immigrants over the past ten years, workforces in the host countries have been growing significantly to the extent that the immigrants represent 70% of the increase in the workforce in Europe, and 47% in the United States as OECD indicates. In the present paper, we attempted to investigate the effect of increased uncertainty caused by the growi...
发表评论
阅读全文

Education Policy Implementation: A Mechanism for Enhancing Primary Education Development in Zanzibar

Education is one of the fundamental rights of individuals; therefore, the government of a country needs to develop and strengthen educational policy and quality as well as to ensure that everyone has equal access to basic education. The improvement of access and quality of education in the world is becoming as an essential factor in development, whereas the basic education (primary school), is acknowledged as a foundation of the higher educational development for every country. To fulfill this goal, governments introduce several policies and procedures; however, it requires some reforms and participation from the politician, policymakers, and other stakeholders to re-examine educational policy so that it can lead to multiplication and betterment of the reforms. Educational reforms actually focus on accountability. A positive educational development and reform is very challenging and needs more effort and strategy on how to use and utilize the resources effectively as such it can achie...
发表评论
阅读全文