1887

Abstract

Summary: Restriction fragment length polymorphisms (RFLPs) detected in total DNA or in rRNA genes are widely used to differentiate strains of bacteria. The changes accounting for these polymorphisms and the extent of genomic difference that they reflect are generally unknown. In this report, several methods have been used to examine the DNA differences between nine isolates. Restriction fragments from total DNA and from rRNA genes were compared between isolates using four and five different restriction enzymes, respectively. The proportion of polymorphic fragments detected was greater with total DNA than with rRNA gene patterns, but depended considerably on the restriction enzyme used. DNA changes underlying nine RFLPs were investigated by using the polymorphic fragments as probes to test for alteration in the position of recognition sites of other enzymes. Two polymorphisms were deduced to result from point mutation in a restriction site. Six were judged to result from DNA rearrangements, five of which involved deletion/insertion of the entire probe fragment. The results demonstrate that DNA rearrangements may be responsible for a high proportion of RFLPs used to differentiate and type strains of bacteria. While this does not limit the utility of such methods, it does preclude calculation of overall DNA sequence conservation from similarities in restriction pattern between isolates. DNA sequence determination of the 16S–23S rRNA intergenic spacer of three isolates revealed minimal base substitutions (less than 1%), suggesting that overall sequence divergence between the isolates may be low.

Loading

Article metrics loading...

/content/journal/micro/10.1099/13500872-140-1-197
1994-01-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/140/1/mic-140-1-197.html?itemId=/content/journal/micro/10.1099/13500872-140-1-197&mimeType=html&fmt=ahah

References

  1. Bacot C.M., Reeves R.H. 1991; Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster. J Bacterial 173:4234–4236
    [Google Scholar]
  2. Barry T., Colleran G., Glennon M., Dunican L.K., Gannon F. 1991; The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Applic 1:51–56
    [Google Scholar]
  3. Bingen E.H., Denamur E., Lambert-Zechovsky N. Y., Bourdois A., Mariani-Kurkdjian P., Cezard J.-P., Navarro J., Elion J. 1991; DNA restriction fragment length polymorphism differentiates crossed from independent infections in nosocomial Xanthomonas maltophilia bacteremia. J Clin Microbiol 29:1348–1350
    [Google Scholar]
  4. Blumberg H. M., Kiehlbauch J.A., Wachsmuth I.K. 1991; Molecular epidemiology of Yersinia enterocolitica 0:3 infections: use of chromosomal DNA restriction fragment length polymorphisms of rRNA genes. J Clin Microbiol 29:2368–2374
    [Google Scholar]
  5. Dice L.R. 1945; Measures of the amount of ecological association between species. Ecology 26:297–302
    [Google Scholar]
  6. Grimont F., Grimont P.A. D. 1986; Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur Microbiol 137B:165–175
    [Google Scholar]
  7. Hall L.M.C., Duke B., Guiney M., Williams R. 1992a; Typing of Enterococcus species by DNA restriction fragment analysis. J Clin Microbiol 30:915–919
    [Google Scholar]
  8. Hall L.M.C., Duke B., Urwin G., Guiney M. 1992b; Epidemiology of Enterococcus faecalis urinary tract infection in a teaching hospital in London, United Kingdom. J Clin Microbiol 30:1953–1957
    [Google Scholar]
  9. Irino K., Grimont F., Casin I., Grimont P. A. D. The Brazilian Purpuric Fever Study Group 1988; rRNA gene restriction patterns of Haemophilus influenzae biogroup aegyptius strains associated with Brazilian purpuric fever. J Clin Microbiol 26:1535–1538
    [Google Scholar]
  10. Janulaitis A. A., Marcinkeviciene L., Petrusyte M., Mironov A. 1981; A new sequence-specific endonuclease from Streptococcus durans . FEBS Lett 134:172–174
    [Google Scholar]
  11. Kado C.I., Liu S.T. 1981; Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145:1365–1373
    [Google Scholar]
  12. Kostman J. R., Edlind T. D., Lipuma J.J., Stull T.L. 1992; Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol 30:2084–2087
    [Google Scholar]
  13. Kristiansen B.-E., Sorensen B., Bjorvatn B., Falk E. S., Fosse E., Bryn K., Froholm L. O., Gaustad P., Bovre K. 1986; An outbreak of group B meningococcal disease: tracing the causative strain of Neisseria meningitidis by DNA fingerprinting. J Clin Microbiol 23:764–767
    [Google Scholar]
  14. Milkman R., Bridges M.M. 1990; Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126:505–517
    [Google Scholar]
  15. Murray B.E., Singh K.V., Markowitz S. M., Lopardo H. A., Patterson J. E., Zervos M. J., Rubeglio E., Eliopoulos G. M., Rice L. B., Goldstein F. W., Jenkins S. G., Caputo G. M., Nasnas R., Moore L. S., Wong E.S., Weinstock G. 1991; Evidence for clonal spread of a single strain of /β—lactamase-producing Enterococcus (Streptococcus) faecalis to six hospitals in five states. J Infect Dis 163:780–785
    [Google Scholar]
  16. Ott M., Bender L., Marre R., Hacker J. 1991; Pulsed field electrophoresis of genomic restriction fragments for the detection of nosocomial Legionella pneumophila in hospital water supplies. J Clin Microbiol 29:813–815
    [Google Scholar]
  17. Owen R.J. 1989; Chromosomal DNA fingerprinting — a new method of species and strain identification applicable to microbial pathogens. J Med Microbiol 30:89–99
    [Google Scholar]
  18. Pitcher D. G., Saunders N.A., Owen R.J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156
    [Google Scholar]
  19. Sambrook J., Fritsch E.F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  20. Stoltzfus A., Leslie J.F., Milkman R. 1988; Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and ton B. . Genetics 120:345–358
    [Google Scholar]
  21. Struelens M. J., Deplano A., Godard C., Maes N., Serruys E. 1992; Epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus by macrorestriction analysis of genomic DNA by using pulsed-field gel electrophoresis. J Clin Microbiol 30:2599–2605
    [Google Scholar]
  22. Stull T. L., Lipuma J.J., Edlind T.D. 1988; A broad spectrum probe for molecular epidemiology of bacteria: ribosomal RNA. J Infect Dis 157:280–286
    [Google Scholar]
  23. Uemori T., Asada K., Kato I., Harasawa R. 1992; Amplification of the 16S–23S spacer region in rRNA operons of Mycoplasmas by the polymerase chain reaction. Syst Appl Microbiol 15:181–186
    [Google Scholar]
  24. Upholt W.B. 1977; Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. Nucleic Acids Res 4:1257–1265
    [Google Scholar]
  25. Williams D. L., Gillis T. P., Portaels F. 1990; Geographically distinct isolates of Mycobacterium leprae exhibit no genotypic diversity by restriction fragment-length polymorphism analysis. Mol Microbiol 4:1653–1659
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/13500872-140-1-197
Loading
/content/journal/micro/10.1099/13500872-140-1-197
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error