Comparison of 16S rDNA analysis and rep-PCR genomic fingerprinting for molecular identification of Yersinia pseudotuberculosis

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 83, Issue 2, 2003, Pages 125-133

  Kim, Wongyong ^a   Song, Mi Ok ^a   Song, Wonkeun ^a,b   Kim, Ki Jung ^a   Chung, Sang In ^a   Choi, Chul Soon ^a   Park, Yong Ha ^c  

^a Chung Ang University College of Medicine   (South Korea)

^b Hallym University   (South Korea)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

16S rDNA; Genus Yersinia; Rep PCR genomic fingerprinting; Yersinia pestis; Yersinia pseudotuberculosis

Indexed keywords

BACTERIAL DNA; DNA 16S; PALINDROMIC DNA;

DNA FINGERPRINTING; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA DETERMINATION; DNA FINGERPRINTING; GENE CLUSTER; GENE SEQUENCE; INTERMETHOD COMPARISON; NEW GENUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; SEQUENCE ANALYSIS; SEROTYPE; SPECIES DIFFERENCE; TAXONOMY; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS;

DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; YERSINIA; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS;

EID: 0038663061     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023301924932     Document Type: Article

References (35)

1. Actman M., Zurth K., Morelli G., Torrea G., Guiyoule A. and Carniel E. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96: 14043-14048.
2. Aleksic S. and Bockemuhl J. 1984. Proposed revision of the Wauters et al. antigenic scheme for serotyping of Yesinia enterocolitica. J. Clin. Microbiol. 20: 99-102.
3. Ash C., Farrow J.A., Dorsch M., Stackebrandt E. and Collins M.D. 1991. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int. J. Syst. Bacteriol. 41: 343-346.
4. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.C. and Struhl K.S. 1993. Current protocols in molecular biology, section 2.4. John Wiely and Sons, New York.
5. Choi C.S., Kim K.J., Kim W.Y. and Chung S.I. 1997. Seropositive rate to Yersinia enterocolitica-pseudotuberculosis complex among patients with acute gastroenteritis in children, 1994-1997. J. Korean Soc. Microbiol. 32: 701-715.
6. Dykhuizen D.E. 2000. Yersinia pestis: an instance species? Trends in Microbiology 8: 198-296.
7. El-Maraghi N.R.H. and Mair N.S. 1979. The histopathology of enteric infection with Yersinia pseudotuberculosis. Am. J. Clin. Pathol. 71: 631-636.
8. Fox G.E., Wisotzkey J.D. and Jurtshuk P. Jr 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166-170.
9. Hulton C.S.J., Higgins C.F. and Sharp P.M. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enteric bacteria. Mol. Microbiol. 5: 825-834.
10. Ibrahim A., Goebel B.M., Liesack W., Griffiths M. and Stackebrandt E. 1993. The phylogeny of the genus Yersinia based on 16S rDNA sequences. FEMS Microbiol. Lett. 114: 173-177.
11. Ibrahim A., Liesack W., Steigerwalt A.G., Brenner D.J., Stackebrandt E. and Robin-Browne R.M. 1997. A cluster of atypical Yersinia strains with a distinctive 16S rDNA signature. FEMS Microbiol. Lett. 146: 73-78.
12. Judd A.K., Schneider M., Sadowsky M.J. and de Bruijin F.J. 1993. Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strain. Appl. Environ. Microbiol. 59: 1702-1708.
13. Knapp W. 1960. Uber weitere antigene Beziehungen zwischen Pasteurella pseudotuberculosis und der Salmonella-Gruppe. Zeitschrift fur Hygiene 146: 315-330.
14. Lane D.J. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E. and Goodfellow M. (eds), Bacterial Systematics. John Wiley & Sons, New York, pp. 115-175.
15. Mair N.S. and Fox E. 1973. An antigenic relationship between Yersinia pseudotuberculosis type 6 and Escherichia coli O-group 55. Cont. Microbiol. Immunol. 2: 180-183.
16. Martin B., Humbert O., Camara M., Guenzi E., Walker J., Mitchell T. et al. 1992. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 20: 3479-3483.
17. Poland J.D., Quan T.J. and Barnes A.M. 1994. Plaque. In: Beran G.W. and Steele J.F. (eds), Handbook of zoonoses. CRC Press, Boca Raton, pp. 93-113.
18. Saitou N. and Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evo. 4: 406-425.
19. Shivaji S., Vijaya Bhanu N. and Aggarwal R.K. 2000. Identification of Yersinia pestis as the causative organism of plaque in India as determined by 16S rDNA sequencing and RAPD-based genomic fingerprinting. FEMS Microbiol. Lett. 189: 247-252.
20. Sneath P.H.A. and Sokal R.R. 1973. Numerical Taxonomy. W.H. Freeman, San Francisco.
21. Stackebrandt E., Liesack W. and Witt D. 1992. Ribosomal RNA and ribosomal DNA sequence analysis. Gene 115: 255-260.
22. Stern M.J., Ames G.F.L., Smith N.H., Robinson E.C. and Higgins C.F. 1984. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37: 1015-1026.
23. Thal E. 1978. The identification of Yersinia pseudotuberculosis. In: Bergan T. and Norris J.R. (eds), Methods in Microbiology Vol. 12. Academic press, London, pp. 2-24.
24. Thal E. and Knapp W. 1971. A revised antigenic scheme of Yersinia pseudotuberculosis. Symp. Series Immunobio. Standard 13: 219-222.
25. Thompson J.D., Higgins D.G. and Gilson T.J. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
26. Trebesius K., Haarmsen D., Rakin A., Schmelz J. and Heesemann J. 1998. Development of rRNA-targeted PCR and in situ hybridization with fluorescently labelled oligonucleosides for detection ofYersinia species. J. Clin. Microbiol. 36: 2557-2564.
27. Tsubokura M. and Aleksic S. 1993. Characterization of Yersinia pseudotuberculosis serogroups O9, O10 and O11; subdivision of O1 serogroup into O1a, O1b, and O1c subgroups. Zbl. Bakt. 278: 500-509.
28. Tsubokura M., Otsuki K., Fukuda T., Kubota M., Imamura M., Itagaki K. et al. 1976. Studies on Yersinia pseudotuberculosis. IV. Isolation of Y. psudotuberculosis from healthy swine. Japanese J. Vet. Sci. 38: 549-552.
29. Tsubokura M., Otsuki K., Kawaoka Y., Fukushima H., Ikemura K. and Kanazawa Y. 1984. Addition of new serogroups and improvement of the antigenic designs of Yersinia pseudotuberculosis. Curr. Microbiol. 11: 89-92.
30. Tyler K.D., Wang G., Tyler S.D. and Johnson W.M. 1997. Factors affecting reliability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J. Clin. Microbiol. 35: 339-346.
31. Van der Zee A., Verbakel H., van Zon J., Frenay I., van Belkum A., Peeters M. et al. 1999. Molecular genotyping of Staphylococcus aureus strains: comparison of repetitive element sequence-based PCR with various typing methods and isolation of novel epidemicity marker. J. Clin. Microbiol. 37: 342-349.
32. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K. and Swings J. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407-438.
33. Versalovic J., Koeuth T. and Lupski J.R. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 9: 6823-6831.
34. Versalovic J., Schneid M., de Brujin F.J. and Lupski J.R. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5: 25-40.
35. Woese C.R. 1987. Bacterial evolution. Microbiol. Rev. 51: 171-221.