Random amplified polymorphic DNA and amplified ribosomal DNA spacer polymorphism: Powerful methods to differentiate Streptococcus thermophilus strains

Journal of Applied Microbiology

Volumn 85, Issue 1, 1998, Pages 25-36

  Moschetti, G ^a   Blaiotta, G ^a   Aponte, M ^a   Catzeddu, P ^b   Villani, F ^a   Deiana, P ^b   Coppola, S ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF SASSARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTER ANALYSIS; DNA; ELECTROPHORESIS; STRAIN;

CONVENTIONAL METHODS; DNA POLYMERASE; MOLECULAR METHODS; POLYMORPHIC DNA; PULSED FIELD GEL ELECTROPHORESIS; REACTION ANALYSIS; RIBOSOMAL DNA; STRAIN TYPING; STREPTOCOCCUS THERMOPHILUS STRAINS; THERMOPHILUS;

POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIUM IDENTIFICATION; DNA DETERMINATION; GENETIC POLYMORPHISM; NONHUMAN; POLYMERASE CHAIN REACTION; PULSED FIELD GEL ELECTROPHORESIS; RANDOM AMPLIFIED POLYMORPHIC DNA; STRAIN DIFFERENCE; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); POSIBACTERIA; STREPTOCOCCUS; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS THERMOPHILUS;

EID: 0031902280     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.1998.00461.x     Document Type: Article

References (42)

1. Barbier, N., Saulnier, P., Chachaty, E., Dumontier, S. and Andremont, A. (1996) Random amplified polymorphic DNA typing versus pulsed-field gel electrophoresis for epidemiological typing of vancomycin-resistant enterococci. Journal of Clinical Microbiology 34, 1096-1099.
2. Barry, T., Colleran, G., Glennon, M., Dunican, L.K. and Gannon, F. (1991) The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods and Applications 1, 51-56.
3. Boutrou, R., Thuault, D. and Bourgeois, C.M. (1995) Identification and characterization of Streptococcus thermophilus strains by pulsed-field gel electrophoresis. Journal of Applied Bacteriology 79, 454-458.
4. Brousseau, R., Saint-Onge, A., Préfontaine, G., Masson, L. and Cabana, J. (1993) Arbitrary primer polymerase chain reaction, a powerful method to identify Bacillus thuringiensis serovars and strains. Applied and Evnironmental Microbiology 59, 114-119.
5. Chachaty, E., Saulnier, P., Martin, A., Mario, N. and Andremont, A. (1994) Comparison of ribotyping, pulsed-field gel electrophoresis and random amplified polymorphic DNA for typing Clostridium difficile strains. FEMS Microbiology Letters 122, 61-68.
6. Cocconcelli, P.S., Porro, D., Galandini, S. and Senini, L. (1995) Development of RAPD protocol for typing of strains of lactic acid bacteria and enterococci. Letters in Applied Microbiology 21, 376-379.
7. Colmin, C., Pebay, M., Simonet, J.M. and Decaris, B. (1991) A species-specific DNA probe obtained from Streptococcus salivarius subsp. thermophilus detects strain restriction polymorphism. FEMS Microbiology Letters 81, 123-128.
8. Coppola, S., Parente, E., Dumontet, S. and La Peccerella, A. (1988) The microflora of natural whey cultures utilized as starters in the manufacture of Mozzarella cheese from water-buffalo milk. Le Lait 68, 295-310.
9. Descheemaeker, P., Lammens, C., Pot, B., Vandamme, P. and Goossens, H. (1997) Evaluation of arbitrarily primed PCR analysis and pulsed-field gel electrophoresis of large genomic DNA fragments for identification of enterococci important in human medicine. International Journal of Systematic Bacteriology 47, 555-561.
10. Du Plessis, E.M. and Dicks, L.M. (1995) Evaluation of random polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii. Current Microbiology 31, 114-118.
11. Facklam, R.R. and Moody, M.D. (1970) Presumptive identification of group D streptococci: the bile-esculin test. Applied Microbiology 20, 245-250.
12. Facklam, R.R. and Sahm, D.F. (1995) Enterococcus. In Manual of Clinical Microbiology, 6th edn. ed. Murray, P.R., Baron, E.J., Pfaller, M.A., Tenover, F.C. and Yolken, R.H. pp. 308-314. Washington, U.C.: American Society for Microbiology.
13. Hall, L.M.C. (1994) Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria? Microbiology 140, 197-204.
14. Hardie, J.M. and Whiley, R.A. (1992) The genus Streptococcus-oral. In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd edn. Vol. 2. pp. 1421-1449 ed. Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Scheifer, K.-H. New York: Springer-Verlag.
15. Hunter, P.R. and Gaston, M.A. (1988) Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. Journal of Clinical Microbiology 26, 2465-2466.
16. Jensen, M.A., Webster, J.A. and Straus, N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Applied and Environmental Microbiology 59, 945-952.
17. McClelland, M., Jones, R., Patel, Y. and Nelson, M. (1987) Restriction endonuclease for pulsed field mapping of bacterial genomes. Nucleic Acids Research 15, 5985-6005.
18. Messner, R., Prillinger, H., Altmann, F., Lopandic, K., Wimmer, K., Molnár, O. and Weigang, F. (1994) Molecular characterization and application of random amplified polymorphic DNA analysis on Mrakia and Sterigmatomyces species. International Journal of Systematic Bacteriology 44, 694-703.
19. Molnár, O., Messner, R., Prillinger, H., Stahl, L. and Slavikova, E. (1995) Genotypic identification of Saccharomyces species using random amplified polymorphic DNA analysis. Systematic and Applied Microbiology 18, 136-145.
20. Naïmi, A., Beck, G. and Branlant, C. (1997) Primary and secondary structures of rRNA spacer regions in enterococci. Microbiology 143, 823-834.
21. Nei, M. and Li, W. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Science, USA 76, 5269-5273.
22. Nour, M., Naimi, A. Beck, G. and Branlant, C. (1995) 16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure. Current Microbiology 31, 270-278.
23. Oberg, C.J. and Broadbent, J.R. (1993) Thermophilic starter cultures: another set of problems. Journal of Dairy Science 76, 2392-2406.
24. Ottogalli, G., Galli, A. and Dellaglio, F. (1979) Taxonomic relationships between Streptococcus thermophilus and some other streptococci. Journal of Dairy Research 46, 127-131.
25. Parente, E. and Moschetti, G. (1997) Starters for mozzarella cheese. In 5th Cheese Symposium ed. Cogan, T.M., Fox, P.F. and Ross, R.P. pp. 31-41. 11-13 March 1997, Cork, Ireland. Dublin: Teagasc.
26. Pébay, M., Roussel, Y., Simonet, J.-M. and Decaris, B. (1992) High-frequency deletion involving closely spaced rRNA gene sets in Streptococcus thermophilus. FEMS Microbiology Letters 98, 51-56.
27. Ramos, M.S. and Harlander, S.K. (1990) DNA fingerprinting of lactococci and streptococci used in dairy fermentations. Applied Microbiology and Biotechnology 34, 368-374.
28. Salzano, G., Moschetti, G., Villani, F. and Coppola, S. (1993) Biotyping of Streptococcus thermophilus strains by DNA fingerprinting. Research in Microbiology 144, 381-387.
29. Salzano, G., Moschetti, G., Villani, F., Pepe, O., Mauriello, G. and Coppola, S. (1994) Genotyping of Streptococcus thermophilus evidenced by restriction analysis of ribosomal DNA. Research in Microbiology 145, 651-658.
30. Saulnier, P., Bourneix, C., Prévost, G. and Andermont, A. (1993) Random amplified polymorphic DNA assay is less discriminating than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus. Journal of Clinical Microbiology 31, 982-985.
31. Schillinger, L. and Lucke, F.-K. (1987) Identification of lactobacilli from meat and meat products. Food Microbiology 4, 199-208.
32. Sperber, W.H. and Swan, J. (1976) Hot loop test for the determination of carbon dioxide production from glucose by lactic acid bacteria. Applied and Environmental Microbiology 31, 990-991.
33. Stephan, R., Schraft, H. and Untermann, F. (1994) Characterization of Bacillus licheniformis with the RAPD technique (randomly amplified polymorphic DNA). Letters in Applied Microbiology 18, 260-263.
34. Systat (1992) Statistics, Version 5.2 Edition. Evanston, IL: Systat Inc.
35. Tilsala-Timisjärvi, A. and Alatossava, T. (1997) Development of oligonucleotide primers from the 16S-23S rRNA intergenic sequences for identifying different dairy and probiotic lactic acid bacteria by PCR. International Journal of Food Microbiology 35, 49-56.
36. Tsakalidou, E., Manopoulou, E., Kabaraki, E., Zoidou, E., Pot, B., Kersters, K. and Kalantzopoulos, G. (1994) The combined use of whole-cell protein extracts for the identification (SDS-PAGE) and enzyme activity screening of lactic acid bacteria isolated from traditional Greek dairy products. Systematic and Applied Microbiology 17, 444-458.
37. Upholt, W.B. (1977) Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. Nucleic Acids Research 4, 1257-1265.
38. Von Krush, U. and Lompe, A. (1982) Schnellest zum qualitativen Nachweis von L (+) und D (-) Milchsaure fur die Bestimmung von Milchesaurebakterien. Milchwissenschaft 37, 65-68.
39. Ward, L.J.H., Brown, J.C.S. and Davey, G.P. (1994) Application of the ligase chain reaction to the detection of nisin A and nisin Z genes in Lactococcus lactis ssp. lactis. FEMS Microbiology Letters 117, 29-34.
40. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18, 7213-7218.
41. Whiley, R.A., Duke, B., Hardie, J.M. and Hall, L.M. (1995) Heterogeneity among 16S-23S rRNA intergenic spacers of species within the 'Streptococcus milleri group'. Microbiology 141, 1461-1467.
42. Williams, G., Kubelik, A., Livak, K., Rafalski, A. and Tingey, S. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531-6535.