Journal of Life Science (생명과학회지)

Korean Society of Life Science (한국생명과학회)
권호 표지
DOI QR코드

DOI QR Code

Change of Sequences and Identification of Chyseobacterium indologenes in Korea by 16S rRNA

16S rRNA에 의한 한국 내 Chyseobacterium indologenes과 염기 서열 변화

  • Huh, Man-Kyu (Department of Molecular Biology, Dongeui University) ;
  • Park, So-Hye (Department of Molecular Biology, Dongeui University) ;
  • Yum, Jong-Hwa (Department of Clinical Laboratory Science, Dongeui University)
  • 허만규 (동의대학교 분자생물학과) ;
  • 박소혜 (동의대학교 분자생물학과) ;
  • 염종화 (동의대학교 임상병리학과)
  • Received : 2011.02.08
  • Accepted : 2011.05.26
  • Published : 2011.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Accurate identification for pathogenic bacterium is an essential element in the clinical microbiology laboratory. We studied molecular analysis involving the identification of Chyseobacterium indologenes and evaluated the seventeen isolates in Korea with the 16S rRNA gene of the ribosome to estimate phylogenetic relationships within the genus Chyseobacterium in GenBank. The aligned data sets for C. indologenes were 1,176 nucleotides. Sequence variation within the C. indologenes was mostly due to nucleotide substitutions. Korean C. indologenes isolates were not strikingly different from the same species found in the other countries. However, the rates of base substitution in Korean C. indologenes isolates were higher than those of other C. indologenes isolates in GenBank. C. indologenes was placed as a sister species to C. isbiliense, C. hominis, C. hispanicum, C. molle, C. hungaricum, and C. pallidum.

병원균에 대한 정확한 동정은 임상 연구실에서 필수적인 요소의 하나이다. Chyseobacterium indologenes에 대한 동정을 포함한 분자생물학적 분석과 리보솜의 16S rRNA 유전자로 한국에서 추출한 17검체와 GenBank에서 Chyseobacterium속 검색을 통해 이들과 계통관계를 평가하였다. C. indologenes의 배당 서열은 1,176 nucleotides였다. C. indologenes 내의 서열 변이는 주로 염기 치환이었다. 한국의 C. indologenes 검체는 다른 나라의 동 종과 크게 다르지 않았다. 그런데 한국의 C. indologenes의 치환율은 GenBank에 있는 동종보다 높았다. C. indologenes는 C. isbiliense, C. hominis, C. hispanicum, C. molle, C. hungaricum, and C. pallidum과 자매종을 형성하였다.

Keywords

References

  1. Bloch, K. C., R. Nadarajah, and R. Jacobs. 1997. Chryseobaterium meninggosepticum : an emerging pathogen among immunocompromised adults. Report of 6 cases and literature review. Medicine (Boltimore) 76, 30-41. https://doi.org/10.1097/00005792-199701000-00003
  2. Bosshard, P. P., R. Zbinden, S. Abels, B. Böddinghaus, M. Altwegg, and E. C. Böttger. 2006. 16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting gram-negative bacteria in the clinical laboratory. J. Clin. Microbiol. 44, 1359-1366. https://doi.org/10.1128/JCM.44.4.1359-1366.2006
  3. Bull, J. J. 1994. Virulence. Evolution 48, 1423-1437. https://doi.org/10.2307/2410237
  4. Cech, T. R. 1988. Conserved sequences and structures of group I introns: building an active site for RNA catalysis - a review. Gene 73, 259-271. https://doi.org/10.1016/0378-1119(88)90492-1
  5. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5s, Distributed by the author. Department of Genetics, Univ. Washington, seattle.
  6. Hsueh, P. R., L. L. Teng, P. C. Yang, S. W. Ho, W. C. Hsieh, and K. T. Luh. 1997. Increasing incidence of nosocomial Chryseobaterium indologennes infections in Taiwan. Eur. J. Clin. Microbiol. Infect. Dis. 16, 568-574. https://doi.org/10.1007/BF02447918
  7. Kirby, J. T., H. S. Sadar, T. R. Walsh, and R. N. Jones. 2004. Antimicrobial susceptibility and epidemiology of a worldwide collection of Chyseobacterium spp. report from the SENTRY antimicrobial survaillance program (1997-2001). J. Clin. Microbiol. 42, 445-448. https://doi.org/10.1128/JCM.42.1.445-448.2004
  8. Kuhsel, M. G., R. Strickland, and J. D. Palmer. 1990. An ancient group I intron shared by eubacteria and chloroplasts. Science 250, 1570-1573. https://doi.org/10.1126/science.2125748
  9. Kumar, S. and S. R. Gadagkar. 2001. Disparity Index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158, 1321-1327.
  10. Michel, F. and B. Dujon. 1983. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members. EMBO J. 2, 33-38.
  11. Nei, M. and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426.
  12. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276, 734-740. https://doi.org/10.1126/science.276.5313.734
  13. Patel, J. B. 2001. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol. Dign. 6, 313-321. https://doi.org/10.2165/00066982-200106040-00012
  14. Rudi, K. and K. S. Jackobsen. 1997. Complex evolutionary patterns of $tRNA_{UAA}^{Leu}$ group I introns in cyanobacterial radiation. J. Bateriol. 181, 3445-3451.
  15. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  16. Schreckenberger, P. C., M. I. Danesshvan, R. S. Weyant, and D. G. Hollis. 2003. Acinetobacter, Achromobacter, Chryseobaterium, Moraxella, and other nonfermentative gram-negative rods, pp. 749-779, In Murray, P. R., E. J. Baron, M. A. Pfaller, J. H. Jorgensen, and R. H. Yolken (eds.), Manual of Clinical microbiology. American Society for Microbiology, Washington, DC.
  17. Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates Inc., Sunderland, MA.
  18. Tajima, F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
  19. Tamura, K., M. Nei, and S. Kumar. 2004. Prospects for inferring very large phylogenies by using neighbor-joining method. Proc. Natl. Acad. Sci. USA 101, 11030-11035. https://doi.org/10.1073/pnas.0404206101
  20. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599. https://doi.org/10.1093/molbev/msm092
  21. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estmating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647-1657. https://doi.org/10.1093/oxfordjournals.molbev.a025892
  22. Tortoli, E. 2003. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacterial of the 199s. Clin. Microbiol. Rev. 16, 319-354. https://doi.org/10.1128/CMR.16.2.319-354.2003
  23. Yannelli, B., I. G. Koj, and B. A. Cunha. 1999. Chyseobacterium meningosepticum bacteremia secondary to central intravenous line-related infection. Am. J. Infet. Control 27, 533-535. https://doi.org/10.1016/S0196-6553(99)70032-5