Analysis of 16S Ribosomal DNA Sequences of Strains and Utilization for Determination of the Phylogeny of the Genus and for Identification of Strains by PCR Free

Abstract

The 16S ribosomal DNAs (rDNAs) of two strains of and one strain of were sequenced. On the basis of phylogenetic analysis data, the genus was placed in the ? subclass of the . The most closely related organism was the intracellular bacterium . The sequenced 16S rDNA molecules of the species exhibited very high levels of similarity (98.5 to 99.9%). Two variable regions, comprising 390 to 450 nucleotides of the 16S rDNA molecules of 17 additional strains, including members of the species and , were also sequenced. At most, six nucleotide differences were observed among the sequences of the strains. The sequence of was virtually identical to the sequences of the strains, thereby supporting the hypothesis that these organisms are members of the same species. On the basis of the observed differences, primer pairs were designed to distinguish strains by using the PCR at the genus, species, and subspecies levels. This permitted sensitive identification of strains belonging to the genus and discrimination of the species and .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-44-1-38
1994-01-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/44/1/ijs-44-1-38.html?itemId=/content/journal/ijsem/10.1099/00207713-44-1-38&mimeType=html&fmt=ahah

References

  1. Bertani G. 1951; Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J. Bacteriol. 62 293 300
    [Google Scholar]
  2. Dams E., Hendriks L., Van de Peer Y., Neefs J.-M., Smits G., Vandenbempt I., de Wächter R. 1988; Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. Suppl. 16 v87 v173
    [Google Scholar]
  3. Dewhirst F. E., Paster B. J., Olsen I., Fraser G. J. 1992; Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J. Bacteriol. 174 2002 2013
    [Google Scholar]
  4. Dorch M., Stackebrandt E. 1992; Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J. Microbiol. Methods 16 271 279
    [Google Scholar]
  5. Eigelsbach H. T., Downs C. M. 1961; Prophylactic effectiveness of live and killed tularemia vaccines. I. Production of vaccine and evaluation in the white mouse and guinea pig. J. Immunol. 87 415 425
    [Google Scholar]
  6. Eigelsbach H. T., McGann V. G. 1984; Gram-negative aerobic cocci. 394 399 Krieg N. R., Holt J. G. Bergey’s manual of systemic bacteriology 1 Williams & Wilkins Co.; Baltimore:
    [Google Scholar]
  7. Felsenstein J. 1989; PHYLIP—phylogeny inference package (version 3.2). Cladistics 5 164 166
    [Google Scholar]
  8. Fitch W. M., Margoliash E. 1967; Construction of phylogenetic trees: a method based on mutational distances as estimated from cytochrome c sequences is of general applicability. Science 155 279 284
    [Google Scholar]
  9. Foreman M., Sandström G., Jaurin B. 1990; Identification of Francisella species and discrimination of type A and type B strains of F. tularensis by 16S rRNA analysis. Appl. Environ. Microbiol. 56 949 955
    [Google Scholar]
  10. Fox G. E., Wisotzkey J. D., 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
    [Google Scholar]
  11. Fry N. K., Warwick S., Saunders N. A., Embley T. M. 1991; The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae. J. Gen. Microbiol. 137 1215 1222
    [Google Scholar]
  12. Hollis D. G., Weaver R. E., Steigerwalt A. G., Wenger J. D., Moss C. W., Brenner D. J. 1989; Francisella philomiragia comb. nov. (formerly Yersinia philomiragia) and Francisella tularensis biogroup novicida (formerly Francisella novicida) associated with human disease. J. Clin. Microbiol. 27 1601 1608
    [Google Scholar]
  13. Hultman T., Ståhl S., Hornes E., Uhlén M. 1989; Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as a support. Nucleic Acids Res. 17 4937 4946
    [Google Scholar]
  14. Kimura M. 1980; A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 111 120
    [Google Scholar]
  15. Marchette N. J., Nicholes P. S. 1961; Virulence and citrulline ureidase activity of Pasteurella tularensis. J. Bacteriol. 82 26 32
    [Google Scholar]
  16. Marconi R. T., Garon C. F. 1992; Phylogenetic analysis of the genus Borrelia: a comparison of North American and European isolates of Borrelia burgdorferi. J. Bacteriol. 174 241 244
    [Google Scholar]
  17. Martinez-Murcia A. J., Benloch S., Collins D. 1992; Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int. J. Syst. Bacteriol. 42 412 421
    [Google Scholar]
  18. Moody M. D., Downs C. M. 1955; Studies on tularemia. I. The relation between certain pathogenic and immunogenic properties of variants of Pasteurella tularensis. J. Bacteriol. 70 297 304
    [Google Scholar]
  19. Murray R. G. E., Brenner D. J., Colwell R. R., de Vos P., Goodfellow M., Grimont P. A. D., Pfennig N., Stackebrandt E., Zavarzin G. A. 1990; Report of the Ad Hoc Committee on Approaches to Taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol. 40 213 215
    [Google Scholar]
  20. Olsufiev N. G., Emelyanova O. S., Dunayeva T. N. 1959; Comparative study of strains of Bacterium tularense. II. Evaluation of criteria of virulence of Bacterium tularense in the old and the new world and their taxonomy. J. Hyg. Epidemiol. Microbiol. Immunobiol. 3 138 149
    [Google Scholar]
  21. Sambrook J., Fritsch E. F., Maniatis T. 1989; Molecular cloning: a laboratory manual. , 2nd ed.. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, N.Y.:
    [Google Scholar]
  22. Sandström G., Sjöstedt A., Foreman M., Pavlovich N. V., Mishankin B. N. 1992; Characterization and classification of strains of Francisella tularensis isolated in the Central Asian focus of the Soviet Union and in Japan. J. Clin. Microbiol. 30 172 175
    [Google Scholar]
  23. Sanger F., Nicklen F., Coulsen A. R. 1977; DNA sequencing with chain termination inhibitors. Proc. Natl. Acad. Sci. USA 74 5463 5469
    [Google Scholar]
  24. Stackebrandt E., Murray R. G. E., Trüper H. G. 1988; Proteobacteria classis nov., a name for the phylogenetic taxon that includes the “purple bacteria and their relatives.” Int. J. Syst. Bacteriol. 38 321 325
    [Google Scholar]
  25. Tärnvik A. 1989; Nature of protective immunity to Francisella tularensis. Rev. Infect. Dis. 11 440 451
    [Google Scholar]
  26. Weisburg W. G., Dobson M. E., Samuel J. E., Dasch G. A., Mallavia L. P., Baca O., Mandelco L., Sechrest J. E., Weiss E., Woese C. R. 1989; Phylogenetic diversity of the rickettsiae. J. Bacteriol. 171 4202 4206
    [Google Scholar]
  27. Weiss E., Dasch G. A., Chang K.-P. 1984; Gram-negative aerobic cocci. 711 713 Krieg N. R., Holt J. G. Bergey’s manual of systemic bacteriology 1 Williams & Wilkins Co.; Baltimore:
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-44-1-38
Loading
/content/journal/ijsem/10.1099/00207713-44-1-38
Loading

Data & Media loading...

Most cited Most Cited RSS feed