Skip to main content
SpringerLink
Log in
Book cover

Bacterial Genomes pp 383–398Cite as

Fingerprinting Bacterial Genomes using Restriction Fragment Length Polymorphisms

  • Chapter

Abstract

The identification of bacterial isolates to the strain level is often necessary for epidemiological and ecological studies to identify and track strains of infectious nature or monitor populations of environmental significance. Typically strains of bacteria have been differentiated on the basis of specific phenotypic traits. Techniques used to delineate strains of bacteria include biotyping, serotyping, bacteriophage typing, antibiotic resistance, or sodium dodecyl sulfate polyacry1-amide gel electrophoresis (SDS-PAGE) patterns for epidemiological (see Pfaller, 1991 and references therein) and ecological studies (see Bottomley, 1992 and references therein). Though these approaches have proven to be useful, each method has inherent disadvantages (see Pfaller, 1991). In the past 10 years there has been an increase in the application of molecular biological techniques, including DNA fingerprinting, to the problems of differentiating and identifying strains of bacteria in the fields of epidemiology and microbial ecology. The advantage of DNA fingerprinting over phenotypic analysis is that the genotype, not the phenotype, is assayed; therefore it is a universally applicable approach for typing anv species of bacteria.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Alsheikhly, A. R., and S. Loefdahl. 1989. Identification of a DNA fragment in the genome of Bordetella pertussis carrying repeated DNA sequences also present in other Bordetella species. Microb. Pathog. 6:193–201.

    Article  PubMed  CAS  Google Scholar 

  • Anand, R. 1986. Pulsed field gel electrophoresis: a technique for fractionating large DNA molecules. Trend Genet. 19:278–283.

    Article  Google Scholar 

  • Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1992. Current protocols in molecular biology. Greene Publishing & Wiley-Interscience, New York.

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Barran, L. R., E.S.P. Bromfield, S. Laberge, and R. Wheatcroft. 1994. Insertion sequence (IS) hybridization supports classification of Rhizobium meliloti by phase typing. Mol. Ecol. 3:267–270.

    Article  CAS  Google Scholar 

  • Barry, T., R. Powell, and F. Gannon. 1990. A general method to generate DNA probes for microorganisms. Bio/technology 8:233–236.

    Article  PubMed  CAS  Google Scholar 

  • Bell, J. A., and S. B. Friedman. 1994. Genetic structure and diversity within local populations of Bacillus mycoides. Evolution 48:1698–1714.

    Article  Google Scholar 

  • Birren, B. W., E. Lai, L. Hood, and M. I. Simon. 1989. Pulsed field gel electrophoresis techniques for separating 1-to 50-kilobase DNA fragments. Anal. Biochem. 177:282–286.

    Article  PubMed  CAS  Google Scholar 

  • Bohm, H., and H. Karch. 1992. DNA fingerprinting of Escherichia coli O157:H7 strains by pulsed-field gel electrophoresis. J. Clin. Microbiol. 30:2169–2172.

    PubMed  CAS  Google Scholar 

  • Bottomley, P. J. 1992. Ecology of Bradyrhizobium and Rhizobium. In Biological Nitrogen Fixation, G. Stacey, R. Burns and H. J. Evans, eds. pp. 293–348. Chapman and Hall, New York.

    Google Scholar 

  • Bove, J. M., and C. Saillard. 1979. Cell biology of spiroplasmas. In The mycoplasmas, R. F. Whitcomb and J. G. Tully, eds. pp. 85–153. Academic Press, New York.

    Google Scholar 

  • Brown, G., Z. Khan, and R. Lifshitz. 1990. Plant growth promoting rhizobacteria: strain identification by restriction fragment length polymorphisms. Can. J. Microbiol. 36:242–248.

    Article  CAS  Google Scholar 

  • Bryner, J. H., I. V. Wesley, and L. A. Pollet. 1988. Restriction enzyme analysis of Campylobacter genomic DNA. Ann. N.Y. Acad. Sci. 529:279–282.

    Article  Google Scholar 

  • Cook, D., E. Barlow, and L. Sequeira. 1989. Genetic diversity of Pseudomonas solanacearum: detection of restriction fragment length polymorphisms with DNA probes that specify virulence and the hypersensitive response. Mol. Plant-Microbe Interact. 2:113–121.

    Article  Google Scholar 

  • Cooksey, D. A., and J. H. Graham. 1989. Genomic fingerprinting of two pathovars of phytopathogenic bacteria by rare-cutting restriction enzymes and field inversion gel electrophoresis. Phytopathology 79:745–750.

    Article  Google Scholar 

  • Demezas, D. H., T. B. Reardon, J. M. Watson, and A. H. Gibson. 1991. Genetic diversity among Rhizobium leguminosarum bv. trifolii strains revealed by allozyme and restriction fragment length polymorphism analyses. Appl. Environ. Microbiol. 57:3489–3495.

    PubMed  CAS  Google Scholar 

  • Denny, T. P., M. N. Gilmour, and R. K. Selander. 1988. Genetic diversity and relationships of two pathovars of Pseudomonas syringae. J. Gen. Microbiol. 134:1949–1960.

    PubMed  CAS  Google Scholar 

  • Festl, H., W. Ludwig, and K.-H. Schleifer. 1986. DNA hybridization probe for the Pseudomonas fluorescens group. Appl. Environ. Microbiol. 52:1190–1194.

    PubMed  CAS  Google Scholar 

  • Galas, D. J., and M. Chandler. 1989. Bacterial insertion sequences. In Mobile DNA, D. E. Berg and M. M. Howe, eds. pp. 109–162. American Society for Microbiology, Washington, D.C.

    Google Scholar 

  • Goh, S. H., S. K. Byrne, J. L. Zhang, and A. W. Chow. 1992. Molecular typing of Staphylo-coccus aureus on the basis of coagulase gene polymorphisms. J. Clin. Microbiol. 30:1642–1645.

    PubMed  CAS  Google Scholar 

  • Grattard, F., J. Etienne, B. Pozzetto, F. Tardy, O. G. Gaudin, and J. Fleurette. 1993. Characterization of unrelated strains of Staphylococcus schleifen by using ribosomal DNA fingerprinting, DNA restriction patterns and plasmid profiles. J. Clin. Microbiol. 31:812–818.

    PubMed  CAS  Google Scholar 

  • Grimont, F., and P.A.D. Grimont. 1991. DNA fingerprinting. In Nucleic acid techniques in bacterial systematics, E. Stackebrandt and M. Goodfellow, eds. pp. 249–279. John Wiley & Sons, New York.

    Google Scholar 

  • Grimont, F., and P.A.D. Grimont. 1986. Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann. Inst. Pasteur/Microbiol. 137B:165–175.

    Article  CAS  Google Scholar 

  • Groman, N., N. Cianciotto, M. Bjorn, and M. Rabin. 1983. Detection and expression of DNA homologous to the tox gene in nontoxinogenic isolates of Corynebacterium diphtheriae. Infect. Immun. 42:48–56.

    PubMed  CAS  Google Scholar 

  • Hahn, M., and H. Hennecke. 1987. Mapping of a Bradyrhizobium japonicum DNA region carrying genes for symbiosis and an asymmetric accumulation of reiterated sequences. Appl. Environ. Microbiol. 53:2247–2252.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Hall, L.M.C., B. Duke, M. Guiney, and R. Williams. 1992. Typing of Enterococcus species by DNA restriction fragment analysis. J. Clin. Microbiol. 30:915–919.

    PubMed  CAS  Google Scholar 

  • Irino, K., F. Grimont, I. Casin, P.A.D. Grimont, and T.B.P.F.S. Group. 1988. rRNA gene restriction patterns of Haemophilus influenzae biogroup aegyptius strains associated with Brazilian purpuric fever. J. Clin. Microbiol. 26:1535–1538.

    PubMed  CAS  Google Scholar 

  • Istock, C. A., K. E. Duncan, N. Ferguson, and X. Zhou. 1992. Sexuality in a natural population of bacteria—Bacillus subtilis challenges the clonal paradigm. Mol. Ecol. 1:95–103.

    Article  PubMed  CAS  Google Scholar 

  • Jordens, J. Z., and L.M.C. Hall. 1988. Characteristics of methicillin-resistant Staphylococcus aureus isolates by restriction endonuclease digestion of chromosomal DNA. J. Med. Microbiol. 27:117–123.

    Article  PubMed  CAS  Google Scholar 

  • Kakoyiannis, C. K., P. J. Winter, and R. B. Marshall. 1984. Identification of Campylobacter coli isolates from animals and humans by bacterial restriction endonuclease DNA analysis. Appl. Environ. Microbiol. 48:545–549.

    PubMed  CAS  Google Scholar 

  • Karlson, U., F. Rojo, J. D. van Elsas, and E. Moore. 1995. Genetic and serological evidence for the recognition of four pentachlorophenol-degrading bacterial strains as a species of the genus Sphingomonas. Syst. Appl. Microbiol. 18:539–548.

    Article  Google Scholar 

  • Lai, E., B. W. Birren, S. M. Clark, M. I. Simon, and L. Hood. 1989. Pulsed field gel electrophoresis. BioTechniques 7:34–42.

    PubMed  CAS  Google Scholar 

  • Lazo, G. R., R. Roffey, and D. W. Gabriel. 1987. Pathovars of Xanthomonas campestris are distinguishable by restriction fragment-length polymorphism. Int. J. Syst. Bacteriol. 37:214–221.

    Article  CAS  Google Scholar 

  • Lefevre, J. C., G. Faucon, A. M. Sicard, and A. M. Gasc. 1993. DNA fingerprinting of Streptococcus pneumoniae strains by pulsed-field gel electrophoresis. J. Clin. Microbiol. 31:2724–2728.

    PubMed  CAS  Google Scholar 

  • Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3:208–218.

    Article  CAS  Google Scholar 

  • McFadden, J. J., P. D. Butcher, J. Thompson, R. Chiodini, and J. Hermon-Taylor. 1987. The use of DNA probes identifying restriction-fragment-length polymorphisms to examine the Mycobacterium avium complex. Mol. Microbiol. 1:283–291.

    Article  PubMed  CAS  Google Scholar 

  • Mielenz, J. R., L. E. Jackson, F. O’Gara, and K. T. Shanmugam. 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 

  • Miranda, A. G., K. V. Singh, and B. E. Murray. 1991. DNA fingerprinting of Enterococcus faecium by pulsed-field gel electrophoresis may be a useful epidemiologic tool. J. Clin. Microbiol. 29:2752–2757.

    PubMed  CAS  Google Scholar 

  • Murphy, G. L., L. C. Robinson, and G. E. Burrows. Restriction endonuclease analysis and ribotyping differentiate Pasteurella haemolytica serotype A1 isolates from cattle within a feedlot. J. Clin. Microbiol. 31:2303–2308.

    Google Scholar 

  • Nass, T., M. Blot, W. M. Fitch, and W. Arber. 1995. Dynamics of IS-related genetic rearrangements in resting Escherichia coli. Mol. Biol. Evol. 12:198–207.

    Google Scholar 

  • Ogle, J. W., J. M. Janda, D. E. Woods, and M. L. Vasil. 1987. Characterization and use of a DNA probe as an epidemiological marker for Pseudomonas aeruginosa. The J. Infect. Dis. 155:119–126.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Pfaller, M. A. 1991. Typing methods for epidemiologic investigation. In Manual of clinical microbiology, A. Balows, J. Hausier, W. J., K. L. Hermann, H. D. Isenberg and H. J. Shadomy, eds. pp. 171–182. American Society for Microbiology, Washington, D.C.

    Google Scholar 

  • Pitcher, D. G., N. A. Saunders, and R. J. Owen. 1989. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8:151–156.

    Article  CAS  Google Scholar 

  • Popovic, T., C. Bopp, O. Olsvik, and K. Wachsmuth. 1993. Epidemiologic application of a standardized ribotype scheme for Vibrio cholera O1. J. Clin. Microbiol. 31:2474–2482.

    PubMed  CAS  Google Scholar 

  • Prevost, G., B. Jaulhac, and Y. Piemont. 1992. DNA fingerprinting by pulsed-field gel electrophoresis is more effective than ribotyping in distinguishing among methicillin-resistant Staphylococcus aureus isolates. J. Clin. Microbiol. 30:967–973.

    PubMed  CAS  Google Scholar 

  • Quinto, C., H. de la Vega, M. Flores, L. Fernandez, C. Ballado, G. Soberon, and R. Palacios. 1982. Reiteration of nitrogen fixation gene sequences in Rhizobium phaseoli. Nature (London) 299:724–726.

    Article  CAS  Google Scholar 

  • Regensburger, A., W. Ludwig, and K.-H. Schleifer. 1988. DNA probes with different specificities from a cloned 23S rRNA gene of Micrococcus luteus. J. Gen. Microbiol. 134:1197–1204.

    PubMed  CAS  Google Scholar 

  • Roberts, R. J. 1988. Restriction enzymes and their isoschizomers. Nucl. Acids Res. 16:r271.

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez-Quinones, F., A. K. Judd, M. J. Sadowsky, R.-L. Liu, and P. B. Cregan. 1992. Hyperreiterated DNA regions are conserved among Bradyrhizobium japonicum serocluster 123 strains. Appl. Environ. Microbiol. 58:1878–1885.

    PubMed  CAS  Google Scholar 

  • Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning:A laboratory manual Cold Spring Harbor: Cold Spring Harbor Laboratory Press.

    Google Scholar 

  • Schmidt, T. M. 1994. Fingerprinting bacterial genomes using ribosomal RNA genes and operons. Methods Mol. Cell. Biol. 5:3–12.

    CAS  Google Scholar 

  • Schofield, P. R., M. A. Djordjevic, B. G. Rolfe, J. Shine, and J. M. Watson. 1983. A molecular linkage map of nitrogenase and nodulation genes in Rhizobium trifolii. Mol. Gen. Genet. 192:459–465.

    Article  CAS  Google Scholar 

  • Schwartz, D. C., and C. R. Cantor. 1984. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75.

    Article  PubMed  CAS  Google Scholar 

  • Sherrat, D. 1989. Tn3 and other related transposable elements: site-specific recombination and transposition. In Mobile DNA, D. E. Berg and M. M. Howe, eds. pp. 163–184. American Society for Microbiology, Washington, D.C.

    Google Scholar 

  • Smith, G. B., and J. M. Tiedje. 1992. Isolation and characterization of nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl. Environ. Microbiol. 58:376–384.

    PubMed  CAS  Google Scholar 

  • Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503–517.

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt, E., and M. Goodfellow. 1991. Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York.

    Google Scholar 

  • Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes. In Nucleic acid techniques in bacterial systematics, E. Stackebrandt and M. Goodfellow, eds. pp. 205–248. John Wiley & Sons, New York.

    Google Scholar 

  • Stanley, J., G. G. Brown, and D.P.S. Verma. 1985. Slow-growing Rhizobium japonicum comprises two highly divergent symbiotic types. J. Bacteriol. 163:148–154.

    PubMed  CAS  Google Scholar 

  • Struelens, M. J., R. Bax, A. Deplano, W.G.V. Quint, and A. van Belkum. 1993a. Concordant clonal delineation of methicillin-resistant Staphylococcus aureus by macrorestriction analysis and polymerase chain reaction genome fingerprinting. J. Clin. Microbiol. 31:1964–1970.

    PubMed  CAS  Google Scholar 

  • Struelens, M. J., V. Schwam, A. Deplano, and D. Baran. 1993b. Genome macrorestriction analysis of diversity and variability of Pseudomonas aeruginosa strains infecting cystic fibrosis patients. J. Clin. Microbiol. 31:2320–2326.

    PubMed  CAS  Google Scholar 

  • Thompson, E., J. V. Leary, and W.W.C. Chun. 1989. Specific detection of Clavibacter michiganense subsp. michiganense by a homologous DNA probe. Phytopathology 79:311–314.

    Article  Google Scholar 

  • Tompkins, L. S., N. Troup, A. Labigne-Roussel, and M. L. Cohen. 1986. Cloned, random chromosomal sequences as probes to identify Salmonella species. J. Infect. Dis. 154:156–162.

    Article  PubMed  CAS  Google Scholar 

  • van Embden, J. D. A., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, and P. M. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406–409.

    PubMed  Google Scholar 

  • Versalovic, J., M. Schneider, F. J. de Bruijn, and J. R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5:25–40.

    CAS  Google Scholar 

  • Wahl, G. M., S. L. Berger, and A. R. Kimmel. 1987. Molecular hybridization of immobilized nucleic acids: theoretical concepts and practical considerations. Methods Enzymol. 152:399–406.

    Article  PubMed  CAS  Google Scholar 

  • Welsh, J., and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 18:7213–7218.

    Article  PubMed  CAS  Google Scholar 

  • Wheatcroft, R., and R. J. Watson. 1988. A positive strain identification method for Rhizobium meliloti. Appl Environ. Microbiol. 54:574–576.

    PubMed  CAS  Google Scholar 

  • Williams, J.G.K., A. R. Kubelik, K. J. Livak, J. A. Rafalski, and S. V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18:6531–6535.

    Article  PubMed  CAS  Google Scholar 

  • Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221–271.

    PubMed  CAS  Google Scholar 

  • Woods, T. C., L. O. Helsel, B. Swaminathan, W. F. Bibb, R. W. Pinner, G. B.G., S. F. Collins, S. H. Waterman, M. W. Reeves, D. J. Brenner, and C. V. Broome. 1992. Characterization of Neisseria meningitidis serogroup C by multilocus enzyme electrophoresis and ribosomal DNA restriction profiles (ribotyping). J. Clin. Microbiol. 30:132–137.

    PubMed  CAS  Google Scholar 

Download references

Authors
  1. David H. Demezas
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824-1312, USA

    Frans J. de Bruijn

  2. Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 609E, Houston, TX, 77030-3498, USA

    James R. Lupski

  3. Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin, Houston, TX, USA, 77030

    George M. Weinstock

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Springer Science+Business Media New York

About this chapter

Cite this chapter

Demezas, D.H. (1998). Fingerprinting Bacterial Genomes using Restriction Fragment Length Polymorphisms. In: de Bruijn, F.J., Lupski, J.R., Weinstock, G.M. (eds) Bacterial Genomes. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-6369-3_31

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-6369-3_31

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-7925-6

  • Online ISBN: 978-1-4615-6369-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation