Jundishapur Journal of Microbiology

Published by: Kowsar

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

Bahram Nasr Esfahani 1 , Sharareh Moghim 1 , Hajieh Ghasemian Safaei 1 , Mohsen Moghoofei 2 , Mansour Sedighi 1 and Shima Hadifar 1 , *
Authors Information
1 Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
2 Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, IR Iran
Article information
  • Jundishapur Journal of Microbiology: April 01, 2016, 9 (4); e30763
  • Published Online: April 16, 2016
  • Article Type: Research Article
  • Received: July 5, 2015
  • Revised: January 18, 2016
  • Accepted: February 1, 2016
  • DOI: 10.5812/jjm.30763

To Cite: Nasr Esfahani B, Moghim S, Ghasemian Safaei H, Moghoofei M, Sedighi M, et al. Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene, Jundishapur J Microbiol. 2016 ; 9(4):e30763. doi: 10.5812/jjm.30763.

Copyright © 2016, Ahvaz Jundishapur University of Medical Sciences. 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. Objectives
3. Materials and Methods
4. Results
5. Discussion
  • 1. de Zwaan R, van Ingen J, van Soolingen D. Utility of rpoB gene sequencing for identification of nontuberculous mycobacteria in the Netherlands. J Clin Microbiol. 2014; 52(7): 2544-51[DOI][PubMed]
  • 2. Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, et al. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet. 2013; 45(2): 172-9[DOI][PubMed]
  • 3. de Jong BC, Antonio M, Gagneux S. Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa. PLoS Negl Trop Dis. 2010; 4(9)[DOI][PubMed]
  • 4. Bouakaze C, Keyser C, Gonzalez A, Sougakoff W, Veziris N, Dabernat H, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based single nucleotide polymorphism genotyping assay using iPLEX gold technology for identification of Mycobacterium tuberculosis complex species and lineages. J Clin Microbiol. 2011; 49(9): 3292-9[DOI][PubMed]
  • 5. Field SK, Cowie RL. Lung disease due to the more common nontuberculous mycobacteria. Chest. 2006; 129(6): 1653-72[DOI][PubMed]
  • 6. Tortoli E. Phylogeny of the genus Mycobacterium: many doubts, few certainties. Infect Genet Evol. 2012; 12(4): 827-31[DOI][PubMed]
  • 7. Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM. Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains). Microb Inform Exp. 2012; 2(1): 7[DOI][PubMed]
  • 8. Mignard S, Flandrois JP. A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees. Int J Syst Evol Microbiol. 2008; 58: 1432-41[DOI][PubMed]
  • 9. Kazumi Y, Mitarai S. The evaluation of an identification algorithm for Mycobacterium species using the 16S rRNA coding gene and rpoB. Int J Mycobacteriol. 2012; 1(1): 21-8[DOI][PubMed]
  • 10. Devulder G, Perouse de Montclos M, Flandrois JP. A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol. 2005; 55: 293-302[DOI][PubMed]
  • 11. Rogall T, Wolters J, Flohr T, Bottger EC. Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol. 1990; 40(4): 323-30[DOI][PubMed]
  • 12. Adekambi T, Berger P, Raoult D, Drancourt M. rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov. Int J Syst Evol Microbiol. 2006; 56: 133-43[DOI][PubMed]
  • 13. Blackwood KS, He C, Gunton J, Turenne CY, Wolfe J, Kabani AM. Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol. 2000; 38(8): 2846-52[PubMed]
  • 14. Bubrick MP, Hitchcock CR. Renal cyst causing afferent loop obstruction and acute pancreatitis. Am Surg. 1975; 41(7): 440-3[PubMed]
  • 15. Varma-Basil M, Garima K, Pathak R, Dwivedi SK, Narang A, Bhatnagar A, et al. Development of a novel PCR restriction analysis of the hsp65 gene as a rapid method to screen for the Mycobacterium tuberculosis complex and nontuberculous mycobacteria in high-burden countries. J Clin Microbiol. 2013; 51(4): 1165-70[DOI][PubMed]
  • 16. Kim BJ, Lee SH, Lyu MA, Kim SJ, Bai GH, Chae GT, et al. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol. 1999; 37(6): 1714-20[PubMed]
  • 17. Khosravi AD, Seghatoleslami S. Genotyping and identification of mycobacteria by fingerprinting techniques. Jundishapur J Microbiol. 2009; 2009(3): 81-91
  • 18. Adekambi T, Drancourt M, Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol. 2009; 17(1): 37-45[DOI][PubMed]
  • 19. Pauls RJ, Turenne CY, Wolfe JN, Kabani A. A high proportion of novel mycobacteria species identified by 16S rDNA analysis among slowly growing AccuProbe-negative strains in a clinical setting. Am J Clin Pathol. 2003; 120(4): 560-6[DOI][PubMed]
  • 20. Rajendhran J, Gunasekaran P. Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res. 2011; 166(2): 99-110[DOI][PubMed]
  • 21. Kim BJ, Lee KH, Park BN, Kim SJ, Bai GH, Kim SJ, et al. Differentiation of mycobacterial species by PCR-restriction analysis of DNA (342 base pairs) of the RNA polymerase gene (rpoB). J Clin Microbiol. 2001; 39(6): 2102-9[DOI][PubMed]
  • 22. Adekambi T, Drancourt M. Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol. 2004; 54: 2095-105[DOI][PubMed]
  • 23. Nasr-Esfahani B, Sarikhani E, Moghim S, et al. Molecular characterization of environmental non-Tuberculous Mycobacteria using PCR- RFLP analysis of 441 Bp heat shock protein 65 fragments Iran J of Public Health 2012; 41(4): 108-114[PubMed]
  • 24. Clarke JD. Cetyltrimethyl ammonium bromide (CTAB) DNA miniprep for plant DNA isolation. Cold Spring Harb Protoc. 2009; 2009(3)[DOI][PubMed]
  • 25. Lee H, Park HJ, Cho SN, Bai GH, Kim SJ. Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J Clin Microbiol. 2000; 38(8): 2966-71[PubMed]
  • 26. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10): 2731-9[DOI][PubMed]
  • 27. Kim BJ, Kim CJ, Chun J, Koh YH, Lee SH, Hyun JW, et al. Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences. Int J Syst Evol Microbiol. 2004; 54: 593-8[DOI][PubMed]
  • 28. Rubin CJ, Thollesson M, Kirsebom LA, Herrmann B. Phylogenetic relationships and species differentiation of 39 Legionella species by sequence determination of the RNase P RNA gene rnpB. Int J Syst Evol Microbiol. 2005; 55: 2039-49[DOI][PubMed]
  • 29. Adekambi T, Colson P, Drancourt M. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol. 2003; 41(12): 5699-708[PubMed]
  • 30. Boor KJ, Duncan ML, Price CW. Genetic and transcriptional organization of the region encoding the beta subunit of Bacillus subtilis RNA polymerase. J Biol Chem. 1995; 270(35): 20329-36[PubMed]
  • 31. Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003; 425(6960): 798-804[DOI][PubMed]
  • 32. Lee JY, Kim SH, Shin JH, Lee H-K, Lee YM, Song SA, et al. Postsurgical Wound Infection Caused by Mycobacterium conceptionense Identified by Sequencing of 16S rRNA, hsp65, and rpoB Genes in an Immunocompetent Patient. Annals of Clinical Microbiology. 2014; 17(1): 23-7[DOI]
  • 33. Yamada-Noda M, Ohkusu K, Hata H, Shah MM, Nhung PH, Sun XS, et al. Mycobacterium species identification--a new approach via dnaJ gene sequencing. Syst Appl Microbiol. 2007; 30(6): 453-62[DOI][PubMed]
  • 34. Simmon KE, Pounder JI, Greene JN, Walsh F, Anderson CM, Cohen S, et al. Identification of an emerging pathogen, Mycobacterium massiliense, by rpoB sequencing of clinical isolates collected in the United States. J Clin Microbiol. 2007; 45(6): 1978-80[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Search Relations:



Create Citiation Alert
via Google Reader

Readers' Comments