A novel means to develop strain-specific DNA probes for detecting bacteria in the environment

Applied and Environmental Microbiology

Volumn 63, Issue 7, 1997, Pages 2863-2869

  Matheson, V Grace ^a   Munakata Marr, Junko ^b   Hopkins, Gary D ^b   Mccarty, Perry L ^b   Tiedje, James M ^a   Forney, Larry J ^a  

^a Michigan State University ^*  (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PALINDROMIC DNA;

ARTICLE; DIAGNOSTIC ACCURACY; DIAGNOSTIC PROCEDURE; DNA PROBE; DNA SEQUENCE; HYBRIDIZATION; MOLECULAR CLONING; STRAIN DIFFERENCE;

BURKHOLDERIA; BURKHOLDERIA CEPACIA;

EID: 0030787489     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.7.2863-2869.1997     Document Type: Article

References (43)

1. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Atlas, R. M., J. F. Williams, and M. K. Huntington. 1995. Legionella contamination of dental-unit waters. Appl. Environ. Microbiol. 61:1208-1213.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1987. Current protocols in molecular biology. John Wiley and Sons, New York, N.Y.
4. Bjourson, A. J., C. E. Stone, and J. E. Cooper. 1992. Combined subtraction hybridization and polymerase chain reaction amplification procedure for isolation of strain-specific Rhizobium DNA sequences. Appl. Environ. Microbiol. 58:2296-2301.
5. Boye, M., T. Ahl, and S. Molin. 1995. Application of a strain-specific rRNA oligonucleotide probe targeting Pseudomonas fluorescens Ag1 in a mesocosm study of bacterial release into the environment. Appl. Environ. Microbiol. 61:1384-1390.
6. Cook, D., and L. Sequeira. 1991. The use of subtractive hybridization to obtain a DNA probe specific for Pseudomonas solanacearum race 3. Mol. Gen. Genet. 227:401-410.
7. de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58:2180-2187.
8. Deneer, H. G., and I. Boychuk. 1991. Species-specific detection of Listeria monocytogenes by DNA amplification. Appl. Environ. Microbiol. 57:606-609.
9. Dimri, G. P., K. E. Rudd, M. K. Morgan, H. Bayat, and G. F.-L. Ames. 1992. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J. Bacteriol. 174:4583-4593.
10. Dunbar, J., I. Zlatkin, and L. Forney. Variation in genome organization among Variovorax paradoxus clones isolated from a single environment. Submitted for publication.
11. Fries, M., L. J. Forney, and J. M. Tiedje. 1997. Phenol- and toluene-degrading populations from an aquifer where successful trichloroethene cometabolism occurred. Appl. Environ. Microbiol. 63:1523-1530.
12. Gannon, F. 1994. DNA probes for the identification of microorganisms. J. Ind. Microbiol. 13:71-76.
13. Hulton, C. S. J., C. F. Higgins, and P. M. Sharp. 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.
14. Jansson, J. 1995. Tracking genetically engineered microorganisms in nature. Curr. Opin. Biotechnol. 6:275-283.
15. Judd, A. K., M. Schneider, M. J. Sadowsky, and F. J. de Bruijn. 1993. Use of repetitive sequences and polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. Appl. Environ. Microbiol. 59:1702-1708.
16. Khan, M. I., B. C. Kirkpatrick, and R. Yamamoto. 1989. Mycoplasma gallisepticum species and strain-specific recombinant DNA probes. Avian Pathol. 18:135-146.
17. Koeuth, T., J. Versalovic, and J. R. Lupski. 1995. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res. 5:408-418.
18. Kogan, S., M. Doherty, and J. Gitschier. 1987. An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. Application to hemophilia A. N. Engl. J. Med. 317:985-990.
19. Lee, C.-Y., S.-F. Pan, and C.-H. Chen. 1995. Sequence of a cloned pR72H fragment and its use for detection of Vibrio parahaemolyticus in shellfish with the PCR. Appl. Environ. Microbiol. 61:1311-1317.
20. Leser, T., M. Boye, and N. B. Hendriksen. 1995. Survival and activity of Pseudomonas sp. strain B13(FR1) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl. Environ. Microbiol. 61:1201-1207.
21. Louws, F. J., D. W. Fullbright, C. T. Stephens, and F. J. de Bruijn. 1994. Pathovar-specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas strains generated with repetitive sequences and PCR. Appl. Environ. Microbiol. 60:2286-2295.
22. Lupski, J. R., and G. M. Weinstock. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174:4525-4529.
23. Mahbubani, M. H., A. K. Bej, R. Miller, L. Haff, J. DiCesare, and R. M. Atlas. 1990. Detection of Legionella with polymerase chain reaction and gene probe methods. Mol. Cell. Probes 4:175-187.
24. Manulis, S., L. Valinsky, A. Lichter, and D. W. Gabriel. 1994. Sensitive and specific detection of Xanthomonas campestris pv. pelargonii with DNA primers and probes identified by random amplified polymorphic DNA analysis. Appl. Environ. Microbiol. 60:4094-4099.
25. Munakata-Marr, J., V. G. Matheson, S. Francesconi, M. S. Shields, L. J. Forney, J. M. Tiedje, P. H. Pritchard, and P. L. McCarty. 1995. Bioaugmentation for in situ cometabolic biodegradation of TCE in groundwater. Presented at the EPA Symposium on Bioremediation of Hazardous Wastes.
26. Munakata-Marr, J., P. McCarty, M. S. Shields, M. Reagin, and S. C. Francesconi. 1996. Enhancement of trichloroethylene degradation in aquifer microcosms bioaugmented with wild type and genetically altered Burkholderia (Pseudomonas) cepacia G4 and PR1. Environ. Sci. Technol. 30:2045-2052.
27. Nascimento, E. R., R. Yamamoto, and M. I. Khan. 1993. Mycoplasma gallisepticum F-vaccine strain-specific polymerase chain reaction. Avian Dis. 37:203-211.
28. Nelson, M. J. K., S. O. Montgomery, E. J. O'Neill, and P. H. Pritchard. 1986. Aerobic metabolism of trichloroethylene by a bacterial isolate. Appl. Environ. Microbiol. 55:383-384.
29. Recorbet, G., C. Picard, P. Normand, and P. Simonet. 1993. Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59:4289-4295.
30. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
31. Seal, S. E., L. A. Jackson, and M. J. Daniels. 1992. Isolation of a Pseudomonas solanacearum-specific DNA probe by subtraction hybridization and construction of species-specific oligonucleotide primers for sensitive detection by the polymerase chain reaction. Appl. Environ. Microbiol. 58:3751-3758.
32. Sharples, G. J., and R. G. Lloyd. 1990. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 18:6503-6508.
33. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503-517.
34. Tas, E. S. K., A. Saano, and K. Lindstrom. 1994. Isolation of a Rhizobium galegae strain-specific DNA probe. Microb. Releases 2:231-237.
35. Thiem, S. M., M. L. Krumme, R. L. Smith, and J. M. Tiedje. 1994. Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer. Appl. Environ. Microbiol. 60:1059-1067.
36. Uyttendaele, M., R. Schukkink, B. van Gemen, and J. Debevere. 1995. Detection of Campylobacter jejuni added to foods by using a combined selective enrichment and nucleic acid sequence-based amplification (NASBA). Appl. Environ. Microbiol. 61:1341-1347.
37. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:6823-6831.
38. Versalovic, J., M. Schneider, F. J. de Bruijn, and J. R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequences based on PCR (rep-PCR). Methods Mol. Cell Biol. 5:25-40.
39. Versalovic, J., V. Kapur, E. O. Mason, Jr., U. Shah, T. Koeuth, J. R. Lupski, and J. M. Musser. 1994. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J. Infect. Dis. 167:850-856.
40. Voytek, M. A., and B. B. Ward. 1995. Detection of ammonium-oxidizing bacteria of the beta subclass of the class proteobacteria in aquatic samples with PCR. Appl. Environ. Microbiol. 61:1444-1450.
41. Woods, C. R., J. Versalovic, T. Koeuth, and J. R. Lupski. 1992. Analysis of relationships among isolates if Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J. Clin. Microbiol. 30:2921-2929.
42. Yamamoto, S., and S. Harayama. 1995. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl. Environ. Microbiol. 61:1104-1109.
43. Zhou, J., and J. M. Tiedje. 1995. Development of phylogenetic probes specific to Burkholderia cepacia G4, p. 65-75. In R. E. Hinchee, G. S. Douglas, and S. K. Ong (ed.), Monitoring and verification of bioremediation. Battelle Press, Columbus, Ohio.