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Application of Total DNA Restriction Pattern Analysis to Identification and Differentiation of Bacterial Strains

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Diagnostic Bacteriology Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 46))

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Abstract

Total DNA restriction pattern analysis is one of the techniques commonly used to identify and group bacteria (1–11). This technique can be used to separate species belonging to the same genus (12,13) or to distinguish highly similar bacterial strains within the same species or subspecies (14–16).

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References

  1. Mielenz, J. R., Jackson, L. E., O’Gara, F., and Shanmugam, K. T. (1979) Fingerprinting bacterial chromosomal DNA with restriction endonuclease EcoRI: comparison of Rhizobium spp. and identification of mutants. Can. J. Microbiol 25, 803–807.

    Article  PubMed  CAS  Google Scholar 

  2. Bjorvatn, B., Lund, V., Kristiansen, B. E., Korsnes, L., Spanne, O., and Lindqvist, B. (1984) Applications of restriction endonuclease fingerprinting of chromosomal DNA of Neisseria meningitidis. J. Clin. Microbiol. 19, 763–765.

    PubMed  CAS  Google Scholar 

  3. Hookey, J. V., Waitkins, S. A., and Jackman, P. J. H. (1985) Numerical analysis of Leptospira DNA-restriction endonuclease patterns. FEMS Microbiol. Lett. 29, 185–188.

    Article  CAS  Google Scholar 

  4. Glynn, P., Higgins, P., Squartini, A., and O’Gara, F. (1985) Strain identification in Rhizobium trifolii using DNA restriction analysis, plasmid DNA profiles and intrinsic antibiotic resistances. FEMS Microbiol. Lett. 30, 177–182.

    Article  CAS  Google Scholar 

  5. Allardet-Servent, A., Bourg, G., Ramuz, M., Pages, M., Bellis, M., and Roizes, G. (1988) DNA polymorphism in strains of the genus Brucella. J. Bacteriol. 170, 4603–4607.

    PubMed  CAS  Google Scholar 

  6. Giovannetti, L., Ventura, S., Bazzicalupo, M., Fani, R., and Materassi, R. (1990) DNA restriction fingerprint analysis of the soil bacterium Azospirillum. J. Gen. Microbiol. 136, 1161–1166.

    PubMed  CAS  Google Scholar 

  7. Degli-Innocenti, F., Ferdani, E., Pesenti-Barili, B., Dani, M., Giovannetti, L., and Ventura, S. (1990) Identification of microbial isolates by DNA fingerprinting: analysis of ATCC Zymomonas strains. J. Biotechnol., 13, 335–346.

    Article  CAS  Google Scholar 

  8. Hernandez, J., Owen, R. J., Costas, M., and Lastovica, A. (1991) DNA-DNA hybridization and analysis of restriction endonuclease and rRNA gene patterns of atypical (catalase-weak/negative) Campylobacter jejuni from paediatric blood and faecal cultures. J. Appl. Bacteriol. 70, 71–80.

    PubMed  CAS  Google Scholar 

  9. Borr, J. D., Ryan, D. A. J., and MacInnes, J. I. (1991) Analysis of Actinobacillus pleuropneumoniae and related organisms by DNA-DNA hybridization and restriction endonuclease fingerprinting. Int. J. Syst. Bacteriol. 41, 121–129.

    Article  PubMed  CAS  Google Scholar 

  10. Baloga, A. O. and Harlander, S. K. (1991) Comparison of methods for discrimination between strains of Listeria monocytogenes from epidemiological surveys. Appl. Environ. Microbiol. 57, 2324–2331.

    PubMed  CAS  Google Scholar 

  11. Giovannetti, L., Fedi, S., Gori, A., Montaini, P., and Ventura, S. (1992) Identification of Azospirillum strains at the genome level with total DNA restriction pattern analysis. System. Appl. Microbiol. 15, 37–41.

    Google Scholar 

  12. Owen, R. J., Costas, M., and Dawson, C. (1989) Application of different chromosomal DNA restriction digest fingerprints to specific and subspecific identification of Campylobacter isolates. J. Clin. Microbiol. 27, 2338–2343.

    PubMed  CAS  Google Scholar 

  13. Ventura, S., Giovannetti, L., Gori, A., Viti, C., and Materassi, R. (1993) Total DNA restriction pattern and quinone composition of members of the family Ectothiorhodospiraceae. System. Appl. Microbiol. 16, 405–410.

    CAS  Google Scholar 

  14. Kristiansen, B. E., Sorensen, B., Simonsen, T., Spanne, O., Lund, V., and Bjorvatn, B. (1984) Isolates of Neisseria meningitidis from different sites in the same patient: phenotypic and genomic studies, with special reference to adherence, piliation, and DNA restriction endonuclease restriction pattern. J. Infect. Dis. 150, 389–396.

    PubMed  CAS  Google Scholar 

  15. Mugnai, L., Giovannetti, L., Ventura, S., and Surico, G. (1994) The grouping of strains of Pseudomonas syringae subsp. savastanoi by DNA restriction fingerprinting. J. Phytopathol. 141

    Google Scholar 

  16. Kristiansen, B. E., Bjorvatn, B., Lund, V., Lindqvist, B., and Holten, E. (1984) Differentiation of B15 strains of Neisseria meningitidis by DNA restriction endonuclease fingerprinting. J. Infect. Dis. 150, 672–676.

    PubMed  CAS  Google Scholar 

  17. Sammons, D. W., Adams, L. D., and Nishizawa, E. E. (1981) Ultrasensitive silver-based color staining of polypeptides in polyacrylamide gels. Electrophoresis 2, 135–141.

    Article  CAS  Google Scholar 

  18. Peterson, E. M. and De La Maza, L. M. (1988) Restriction endonuclease analysis of DNA from Chlamydia trachomatis biovars. J. Clin. Microbiol. 26, 625–629.

    PubMed  CAS  Google Scholar 

  19. McCormick, W. A., Stevenson, R. M. W., and MacInnes, J. I. (1990) Restriction endonuclease fingerprinting analysis of Canadian isolates of Aeromonas salmonicida. Can. J. Microbiol. 36, 24–32.

    Article  PubMed  CAS  Google Scholar 

  20. Wesley, I. V. and Ashton, F. (1991) Restriction enzyme analysis of Listeria monocytogenes strains associated with food-borne epidemics. Appl. Environ. Microbiol. 57, 969–975.

    PubMed  CAS  Google Scholar 

  21. Ståhl, M., Molin, G., Persson, A., Ahrné, S., and Ståhl, S. (1990) Restriction endonuclease patterns and multivariate analysis as a classification tool for Lactobacillus spp. Int. J. Syst. Bacteriol. 40, 189–193.

    Article  Google Scholar 

  22. Ramos, M. S. and Harlander, S. K. (1990) DNA fingerprinting of lactococci and streptococci used in dairy fermentation. Appl. Microbiol. Biotechnol., 34, 368–374.

    Article  CAS  Google Scholar 

  23. Bialkowska-Hobrzanska, H., Jaskot, D., and Hammerberg, O. (1990) A method for DNA restriction endonuclease fingerprinting of coagulase negative staphylococci. J. Microb. Meth. 12, 41–49.

    Article  CAS  Google Scholar 

  24. Hartmann, A. and Amarger, N. (1991) Genotypic diversity of an indigenous Rhizobium meliloti field population assessed by plasmid profiles, DNA fingerprinting, and insertion sequence typing. Can. J. Microbiol. 37, 600–608.

    Article  CAS  Google Scholar 

  25. Owen, R. J., Bickley, J., Moreno, M., Costas, M., and Morgan, D. R. (1991) Biotype and macromolecular profiles of cytotoxin-producing strains of Helicobacter pylori from antral gastric mucosa. FEMS Microbiol. Lett. 79, 199–204.

    Article  CAS  Google Scholar 

  26. Ogden, R. C. and Adams, D. H. (1987) Electrophoresis in agarose and acrylamide gels, in Guide to Molecular Cloning Techniques, vol. 152 (Berger, S. L. and Kimmel, A. R., eds.), Academic, Orlando FL, pp. 61–90.

    Chapter  Google Scholar 

  27. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

    Google Scholar 

  28. Walker, J. M. (ed.) (1984) Methods in Molecular Biology, Vol. 2: Nucleic Acids. Humana, Clifton, NJ.

    Google Scholar 

  29. Walker, J. M. (ed.) (1988) Methods in Molecular Biology, Vol 4: New Nucleic Acid Techniques, Humana, Clifton, NJ.

    Google Scholar 

  30. Forbes, K. J., Bruce, K. D., Jordens, J. Z., Ball, A., and Pennington, T. H. (1991) Rapid methods in bacterial DNA fingerprinting. J. Gen. Microbiol. 137, 2051–2058.

    PubMed  CAS  Google Scholar 

  31. Sneath, P. H. A. and Sokal, R. R. (1973) Numerical Taxonomy The Principles and Practice of Numerical Classification, Freeman, San Francisco.

    Google Scholar 

  32. SAS Institute Inc. (1987) SAS/STAT Guide for Personal Computer, Version 6, Author, Cary, NC.

    Google Scholar 

  33. Vauterin, L. and Vauterin, P. (1992) A new system for standardization and objective comparison of electrophoresis patterns: application in bacterial identification, in Proceedings of the Conference on Taxonomy and Automated Identification of Bacteria (Schindler, J., ed.), Prague, Czech Republic, pp. 19–22.

    Google Scholar 

  34. Gentzbittel, L. and Nicolas, P. (1989) A basic program to construct evolutionary trees from restriction endonuclease data. J. Hered. 80, 254.

    Google Scholar 

  35. Gentzbittel, L. and Nicolas, P. (1990) Improvement of “a BASIC program to construct evolutionary trees from restriction endonuclease data” with the use of PASCAL. J. Hered. 81, 491,492.

    PubMed  CAS  Google Scholar 

  36. Sorensen, B., Falk, E. S., Wisloff-Nilsen, E., Bjorvatn, B., and Kristiansen, B. E. (1985) Multivariate analysis of Neisseria DNA restriction endonuclease pattern. J. Gen. Microbiol. 131, 3099–3104.

    PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Dipartimento di Agreobiologia e Agrochimica, Universita della Tuscia, Viterbo, Italy

    Luciana Giovannetti

  2. Centro di Studio dei Microorganismi Autotrofi, Firenze, Italy

    Stefano Ventura

Authors
  1. Luciana Giovannetti
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  2. Stefano Ventura
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Editor information

Editors and Affiliations

  1. Dalgety plc, Cambridge, UK

    Jenny Howard

  2. Department of Medicine, University of Cambridge, UK

    David M. Whitcombe

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© 1995 Humana Press Inc.

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Giovannetti, L., Ventura, S. (1995). Application of Total DNA Restriction Pattern Analysis to Identification and Differentiation of Bacterial Strains. In: Howard, J., Whitcombe, D.M. (eds) Diagnostic Bacteriology Protocols. Methods in Molecular Biology™, vol 46. Humana Press. https://doi.org/10.1385/0-89603-297-3:165

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  • DOI: https://doi.org/10.1385/0-89603-297-3:165

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-297-2

  • Online ISBN: 978-1-59259-533-4

  • eBook Packages: Springer Protocols

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