Avicenna Journal of Clinical Microbiology and Infection

Published by: Kowsar

Exploration of Specific DNA-Barcodes in Shigella dysenteriae Using In-silico Analysis

Authors Information
1 Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
2 Young Researchers and Elite Club, Science and Research Branch, Islamic Azad University, Tehran, Iran
3 Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
4 Department of Virology, Tarbiat Modares University, Tehran, Iran
Article Notes and Dates
Avicenna Journal of Clinical Microbiology and Infection: November 2017, 4 (4); e13082.Published Online: August 31, 2017
Article Type: Research Article; Received : March 14, 2017; Revised : May 13, 2017; Accepted : July 17, 2017
DOI: http://dx.doi.org/10.5812/ajcmi.13082

To Cite : Kamali M, Bakhshi B, Salimi A, Mohseni Fard E, Darvishi M H, et al. Exploration of Specific DNA-Barcodes in Shigella dysenteriae Using In-silico Analysis, Avicenna J Clin Microb Infec. 2017 ;4(4):e13082. doi: 10.5812/ajcmi.13082.

Copyright: Copyright © 2017, Avicenna Journal of Clinical Microbiology and Infection. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Methods
3. Results
4. Discussion
  • 1. Kotloff KL, Winickoff JP, Ivanoff B, Clemens JD, Swerdlow DL, Sansonetti PJ, et al. Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ. 1999; 77(8): 651-66[PubMed]
  • 2. Pothoulakis C, Lamont JT. Microbes and microbial toxins: paradigms for microbial-mucosal interactions II. The integrated response of the intestine to Clostridium difficile toxins. Am J Physiol Gastrointest Liver Physiol. 2001; 280(2)-83[PubMed]
  • 3. DuPont HL, Levine MM, Hornick RB, Formal SB. Inoculum size in shigellosis and implications for expected mode of transmission. J Infect Dis. 1989; 159(6): 1126-8[PubMed]
  • 4. Li Y, Cao B, Liu B, Liu D, Gao Q, Peng X, et al. Molecular detection of all 34 distinct O-antigen forms of Shigella. J Med Microbiol. 2009; 58: 69-81[DOI][PubMed]
  • 5. Martinez-Becerra FJ, Kissmann JM, Diaz-McNair J, Choudhari SP, Quick AM, Mellado-Sanchez G, et al. Broadly protective Shigella vaccine based on type III secretion apparatus proteins. Infect Immun. 2012; 80(3): 1222-31[DOI][PubMed]
  • 6. Torres AG. Current aspects of Shigella pathogenesis. Rev Latinoam Microbiol. 2004; 46(3-4): 89-97[PubMed]
  • 7. Sansonetti PJ, Kopecko DJ, Formal SB. Involvement of a plasmid in the invasive ability of Shigella flexneri. Infect Immun. 1982; 35(3): 852-60[PubMed]
  • 8. Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun. 2003; 71(5): 2775-86[PubMed]
  • 9. Jin Q, Yuan Z, Xu J, Wang Y, Shen Y, Lu W, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002; 30(20): 4432-41[PubMed]
  • 10. Maurelli AT, Fernandez RE, Bloch CA, Rode CK, Fasano A. "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci U S A. 1998; 95(7): 3943-8[PubMed]
  • 11. Gangarosa EJ, Perera DR, Mata LJ, Mendizabal-Morris C, Guzman G, Reller LB. Epidemic Shiga bacillus dysentery in Central America. II. Epidemiologic studies in 1969. J Infect Dis. 1970; 122(3): 181-90[PubMed]
  • 12. Mendizabal-Morris CA, Mata LJ, Gangarosa EJ, Guzman G. Epidemic Shiga-bacillus dysentery in Central America. Derivation of the epidemic and its progression in Guatemala, 1968-69. Am J Trop Med Hyg. 1971; 20(6): 927-33[PubMed]
  • 13. Nie H, Yang F, Zhang X, Yang J, Chen L, Wang J, et al. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics. 2006; 7: 173[DOI][PubMed]
  • 14. Mata LJ, Gangarosa EJ, Caceres A, Perera DR, Mejicanos ML. Epidemic Shiga bacillus dysentery in Central America. I. Etiologic investigations in Guatemala, 1969. J Infect Dis. 1970; 122(3): 170-80[PubMed]
  • 15. Venkatesan MM, Hartman AB, Newland JW, Ivanova VS, Hale TL, McDonough M, et al. Construction, characterization, and animal testing of WRSd1, a Shigella dysenteriae 1 vaccine. Infect Immun. 2002; 70(6): 2950-8[PubMed]
  • 16. Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A. 2000; 97(19): 10567-72[DOI][PubMed]
  • 17. Zhang Y, Lin K. A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. BMC Evol Biol. 2012; 12: 174[DOI][PubMed]
  • 18. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009; 5(1)[DOI][PubMed]
  • 19. Donnenberg MS. Escherichia coli: virulence mechanisms of a versatile pathogen. 2002;
  • 20. Lan R, Lumb B, Ryan D, Reeves PR. Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli. Infect Immun. 2001; 69(10): 6303-9[DOI][PubMed]
  • 21. Amani J, Ahmadpour A, Imani Fooladi AA, Nazarian S. Detection of E. coli O157:H7 and Shigella dysenteriae toxins in clinical samples by PCR-ELISA. Braz J Infect Dis. 2015; 19(3): 278-84[DOI][PubMed]
  • 22. Binet R, Deer DM, Uhlfelder SJ. Rapid detection of Shigella and enteroinvasive Escherichia coli in produce enrichments by a conventional multiplex PCR assay. Food Microbiol. 2014; 40: 48-54[DOI][PubMed]
  • 23. Newland JW, Neill RJ. DNA probes for Shiga-like toxins I and II and for toxin-converting bacteriophages. J Clin Microbiol. 1988; 26(7): 1292-7[PubMed]
  • 24. Faruque SM, Khan R, Kamruzzaman M, Yamasaki S, Ahmad QS, Azim T, et al. Isolation of Shigella dysenteriae type 1 and S. flexneri strains from surface waters in Bangladesh: comparative molecular analysis of environmental Shigella isolates versus clinical strains. Appl Environ Microbiol. 2002; 68(8): 3908-13[PubMed]
  • 25. Kislyuk AO, Haegeman B, Bergman NH, Weitz JS. Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics. 2011; 12: 32[DOI][PubMed]
  • 26. Lan Y, Morrison JC, Hershberg R, Rosen GL. POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes. Nucleic Acids Res. 2014; 42-32[DOI][PubMed]
  • 27. Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, et al. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res. 2013; 41-47[DOI][PubMed]
  • 28. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. Nucleic Acids Symp Ser. 1999; 41(2): 95-8
  • 29. Tao T. Program Parameters for blastall. View Article PubMed/NCBI Google Scholar. 2006;
  • 30. Yang J, Chen L, Yu J, Sun L, Jin Q. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 2006; 34-401[DOI][PubMed]
  • 31. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005; 33-8[DOI][PubMed]
  • 32. Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics. 2011; 12: 116[DOI][PubMed]
  • 33. Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ. PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics. 2008; 9: 170[DOI][PubMed]
  • 34. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002; 30(11): 2478-83[PubMed]
  • 35. Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol. 2007; 73(1): 278-88[DOI][PubMed]
  • 36. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, et al. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol. 2012; 10(8)[DOI][PubMed]
  • 37. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, et al. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010; 3(3): 249-53[DOI][PubMed]
  • 38. Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 2013; 7(8): 1493-506[DOI][PubMed]
  • 39. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, et al. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol. 2010; 76(12): 3886-97[DOI][PubMed]
  • 40. Achenbach LA, Carey J, Madigan MT. Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Appl Environ Microbiol. 2001; 67(7): 2922-6[DOI][PubMed]
  • 41. Walsh DA, Bapteste E, Kamekura M, Doolittle WF. Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol. 2004; 21(12): 2340-51[DOI][PubMed]
  • 42. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008; 9(10)[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Cited By:

Search Relations:


  • Mehdi Kamali: [PubMed] [Scholar]
  • Behnam Bakhshi: [PubMed] [Scholar]
  • Ali Salimi: [PubMed] [Scholar]
  • Ehsan Mohseni Fard: [PubMed] [Scholar]
  • Mohammad Hasan Darvishi: [PubMed] [Scholar]
  • Elahe Ehghaghi: [PubMed] [Scholar]
  • Related Article in PubMed
  • Related Article in Google Scholar

Create Citiaion Alert via Google Reader