Skip to main content
SpringerLink
Log in

Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes

  • Chapter
Bacterial Genomes

Abstract

Bacterial chromosomes contain multiple interspersed repetitive sequences that occupy intergenic regions at sites dispersed throughout the genome. Such blocks of noncoding, repetitive sequences can serve as multiple genetic targets for oligonucleotide probes, enabling the generation of unique DNA profiles or fingerprints for individual bacterial strains. DNA fingerprinting requires the resolution of differently sized DNA fragments derived from chromosomal or plasmid DNA by restriction endonuclease-mediated digestion and/or DNA amplification to yield a band pattern that serves as a unique identifier. These unique “bar codes” or DNA fingerprints define each bacterial chromosome without the need for measuring gene expression or enzyme function. Genotypic or molecular approaches differ with respect to the level of resolution of individual bacterial species or strains into distinct categories (Figure 34-1).

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

Access this chapter

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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Clarridge, J. E., T. J. Raich, D. Pirwani, B. Simon, L. Tsai, M. C. Rodriguez-Barradas, R. Regnery, A. Zollo, D. C. Jones, and C. Rambo. 1995. Strategy to detect and identify Bartonella species in routine clinical laboratory yields Bartonella henselae from human immunodeficiency virus-positive patient and unique Bartonella strain from his cat. J. Clin. Microbiol. 33:2107–2113.

    PubMed  Google Scholar 

  • Colman, S. D., P. C. Hu, and K. F. Bott. 1990. Prevalence of novel repeat sequences in and around the P1 operon in the genome of Mycoplasma pneumoniae. Gene 87:91–96.

    Article  PubMed  CAS  Google Scholar 

  • Correia, F. F., S. Inouye, and M. Inouye. 1986. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA. J. Bacteriol. 167:1009–1015.

    PubMed  CAS  Google Scholar 

  • de Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic element and enterobacterial repetitive intergenic consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58:2180–2187.

    PubMed  Google Scholar 

  • de Bruijn, F. J., M. Schneider, U. Rossbach, and F. J. Louws. 1995. Automated fluorescent and conventional rep-PCR genomic fingerprinting and multiplex PCR to classify bacteria and track genes. In: Proceedings of the Seventh International Symposium on Microbial Ecology. Anonymous, Brazil.

    Google Scholar 

  • Del Vecchio, V. G., J. M. Petroziello, M. J. Gress, F. K. McCleskey, G. P. Melcher, H. K. Crouch, and J. R. Lupski. 1995. Molecular genotyping of methicillin-resistant Staphylococcus aureus via fluorophore-enhanced repetitive-sequence PCR. J. Clin. Microbiol. 33:2141–2144.

    PubMed  Google Scholar 

  • Dunn, W. M., Jr., and S. Maisch. 1995. Epidemiological investigation of infections due to Alcaligenes species in children and patients with cystic fibrosis: Use of repetitive-element-sequence polymerase chain reaction. Clin. Infect. Dis. 20:836–841.

    Article  Google Scholar 

  • Edel, V., C. Steinberg, I. Avelange, G. Laguerre, and C. Alabouvette. 1995. Comparison of three molecular methods for the characterization of Fusarium oxyxporum strains. Phytopathol. 85:579–585.

    Article  CAS  Google Scholar 

  • Ellsworth, D. L., K. D. Rittenhouse, and R. L. Honeycutt. 1993. Artifactual variation in randomly amplified polymorphic DNA banding patterns. Biotechniques 14:214–217.

    PubMed  CAS  Google Scholar 

  • Endtz, H. P., B.A.J. Giesendorf, A. van Belkum, S.J.M. Lauwers, W. H. Jansen, and W.G.V. Quint. 1993. PCR-mediated DNA typing of Campylobacter jejuni isolated from patients with recurrent infections. Res. Microbiol. 144:703–708.

    Google Scholar 

  • Forsyth, M. H., and S. J. Geary. 1996. The repetitive element Rep MP 1 of Mycoplasma pneumoniae exists as a core element within a larger, variable repetitive mosaic. J. Bacteriol. 178:917–921.

    PubMed  CAS  Google Scholar 

  • Georghiou, P., R. J. Hamill, C. E. Wright, J. Versalovic, T. Koeuth, D. A. Watson, and J. R. Lupski. 1995. Molecular epidemiology of infections due to Enterobacter aerogenes: Identification of hospital outbreak strains by molecular techniques. Clin. Infect. Dis. 20:84–94.

    Article  PubMed  CAS  Google Scholar 

  • Georghiou, P. R., A. M. Doggett, M. A. Kielhofner, J. E. Stout, D. A. Watson, J. R. Lupski, and R. J. Hamill. 1994. Molecular fingerprinting of Legionella species by repetitive element PCR. J. Clin. Microbiol. 32:2989–2994.

    PubMed  CAS  Google Scholar 

  • Giesendorf, B.A.J., A. van Belkum, A. Koeken, H. Stegeman, M.H.C. Henkens, J. Van der Plas, H. Goossens, H.G.M. Niesters, and W.G.V. Quint. 1993. Development of species-specific DNA probes for Campylobacter jejuni, Campylobacter coli, and Campylobacter lari by polymerase chain reaction fingerprinting. J. Clin. Microbiol. 31:1541–1546.

    PubMed  CAS  Google Scholar 

  • Go, M., K. Chan, J. Versalovic, T. Koeuth, D. Y. Graham, and J. R. Lupski. 1995. Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations. Scand. J. Gastroenterol. 30:640–646.

    Article  PubMed  CAS  Google Scholar 

  • Harvey, B. S., T. Koeuth, J. Versalovic, C. R. Woods, and J. R. Lupski. 1995. Vertical transmission of Citrobacter diversus documented by DNA fingerprinting. Infect. Control Hosp. Epidemiol. 16:564–569.

    Article  PubMed  CAS  Google Scholar 

  • Jordens, J. Z., J. Paul, J. Bates, C. Beaumont, J. Kimari, and C. Gilks. 1995. Characterization of Streptococcus pneumoniae from human immunodeficiency virus-seropositive patients with acute and recurrent pneumonia. J. Infect. Dis. 172:983–987.

    Article  PubMed  CAS  Google Scholar 

  • Judd, A. K., M. Schneider, M. J. Sadowsky, and F. J. de Bruijn. 1993. Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. Appl. Environ. Microbiol. 59:1702–1708.

    PubMed  CAS  Google Scholar 

  • Koeuth, T., J. Versalovic, and J. R. Lupski. 1995. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Research 5:408–418.

    Article  PubMed  CAS  Google Scholar 

  • Leung, K., S. R. Strain, F. J. de Bruijn, and P. J. Bottomley. 1994. Genotypic and phenotypic comparisons of chromosomal types within an indigenous soil population of Rhizobium leguminosarum bv. trifolii. Appl. Environ. Microbiol. 60:416–426.

    PubMed  CAS  Google Scholar 

  • Louws, F. J., D. W. Fulbright, C. T. Stephens, and F. J. de Bruijn. 1994. Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl. Environ. Microbiol. 60:2286–2295.

    PubMed  CAS  Google Scholar 

  • Louws, F. J., D. W. Fulbright, C. Taylor Stephens, and F. J. de Bruijn. 1995. Differentiation of genomic structure by rep-PCR fingerprinting to rapidly classify Xanthomonas campestris pv. vesicatoria. Mol. Plant Pathol. 85:528–536.

    CAS  Google Scholar 

  • Louws, F. J., M. Schneider, and F. J. de Bruijn. 1996. Assessing genetic diversity of microbes using repetitive sequence-based PCR (rep-PCR). In Environmental Applications of Nucleic Acid Amplifications Techniques. pp. 63–64. G. Toranzos, ed. Technomic Publishing Co., Lancaster, PA.

    Google Scholar 

  • Lupski, J. R., and G. M. Weinstock. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174:4525–4529.

    PubMed  CAS  Google Scholar 

  • McManus, P. S., and A. L. Jones. 1995. Genetic fingerprinting of Erwinia amylovora strains isolated from tree-fruit crops and Rubus spp. Phytopathology 85:1547–1553.

    Article  CAS  Google Scholar 

  • Nick, G., and K. Lindstrom. 1994. Use of repetitive sequences and the polymerase chain reaction to fingerprint the genomic DNA of Rhizobium galegae strains and to identify the DNA obtained by sonicating the liquid cultures and root nodules. System. Appl. Microbiol. 17:265–273.

    Article  CAS  Google Scholar 

  • Opgenorth, D. C., C. D. Smart, F. J. Louws, F. J. de Bruijn, and B. C. Kirkpatrick. 1996. Identification of Xanthomonas fragariae field isolates by rep-PCR genomic fingerprinting. Plant Disease 80:868–873.

    Article  Google Scholar 

  • Poh, C. L., V. Ramachandran, and J. W. Tapsall. 1996. Genetic diversity of Neisseria gonorrhoeae IB-2 and IB-6 isolates revealed by whole-cell repetitive element sequence-based PCR. J. Clin. Microbiol. 34:292–295.

    PubMed  CAS  Google Scholar 

  • Ralph, D., M. McClelland, J. Welsh, G. Baranton, and P. Perolat. 1993. Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rRNA genes. J. Bacteriol. 175:973–981.

    Google Scholar 

  • Reboli, A. C., E. D. Houston, J. S. Monteforté, C. A. Wood, and R. J. Hamill. 1994. Discrimination of epidemic and sporadic isolates of Acinetobacter baumannii by repetitive element PCR-mediated DNA fingerprinting. J. Clin. Microbiol. 32:2635–2640.

    PubMed  CAS  Google Scholar 

  • Rivera, I. G., M.A.R. Chowdhury, A. Huq, D. Jacobs, M. T. Martins, and R. R. Colwell. 1995. Enterobacterial repetitive intergenic consensus sequences and the PCR to generate fingerprints of genomic DNAs from Vibrio cholerae O1, O139, and non-01 strains. Appl. Environ. Microbiol. 61:2898–2904.

    PubMed  CAS  Google Scholar 

  • Rodriguez-Barradas, M. C., R. J. Hamill, E. D. Houston, P. R. Georghiou, J. E. Clarridge, R. L. Regnery, and J. E. Koehler. 1995. Genomic fingerprinting of Bartonella species by repetitive element PCR for distinguishing species and isolates. J. Clin. Microbiol. 33:1089–1093.

    PubMed  CAS  Google Scholar 

  • Rossbach, S., G. Rasul, M. Schneider, B. Eardley, and F. J. de Bruijn. 1995. Structural and functional conservation of the rhizopine catabolism (moc) locus is limited to selected Rhizobium meliloti strains and unrelated to their geographical origin. Mol. Plant Micr. Interact. 8:549–559.

    Article  CAS  Google Scholar 

  • Schneider, M., and F. J. de Bruijn. 1996. Rep-PCR mediated genomic fingerprinting of rhizobia and computer assisted phylogenetic pattern analysis. World J. Microbiol. Biotechnol. 12:163–174.

    Article  CAS  Google Scholar 

  • Sneath, P.H.A., and R. R. Sokal. 1973. Numerical Taxonomy. Freeman, San Francisco.

    Google Scholar 

  • Snelling, A. M., P. Gerner-Smidt, P. M. Hawkey, J. Heritage, P. Parnell, C. Porter, A. R. Bodenham, and T. Inglis. 1996. Validation of use of whole-cell repetitive extragenic palindromic sequence-based PCR (REP-PCR) for typing strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex and application of the method to the investigation of a hospital outbreak. J. Clin. Microbiol. 34:1193–1202.

    PubMed  CAS  Google Scholar 

  • Sokal, R. R., and P.H.A. Sneath. 1963. Principles of Numerical Taxonomy. WH Freeman and Company, San Francisco.

    Google Scholar 

  • Stern, M. J., G.F.L. Ames, N. H. Smith, E. C. Robinson, and C. F. Higgins. 1984. Repetitive extragenic palindromic sequences: A major component of the bacterial genome. Cell 37:1015–1026.

    Article  PubMed  CAS  Google Scholar 

  • Strain, S. R., K. Leung, T. S. Whittam, F. J. de Bruijn, and P. J. Bottomley. 1994. Genetic structure of Rhizobium leguminosarum biovar trifolii and viciae populations found in two Oregon soils under different plant communities. Appl. Environ. Microbiol. 60:2772–2778.

    PubMed  CAS  Google Scholar 

  • Struelens, M. J., R. Bax, A. Deplano, W.G.V. Quint, and A. van Belkum. 1993. 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 

  • Taylor, N. S., J. G. Fox, N. S. Akopyants, D. E. Berg, N. Thompson, B. Shames, L. Yan, E. Fontham, F. Janney, F. M. Hunter, and P. Correa. 1995. Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J. Clin. Microbiol. 33:918–923.

    PubMed  CAS  Google Scholar 

  • van Belkum, A., R. Bax, P. Peerbooms, W. H. Goessens, N. van Leeuwen, and W.G.L. Quint. 1993a. Comparison of phage typing and DNA fingerprinting by polymerase chain reaction for discrimination of methicillin-resistant Staphylococcus aureus strains. J. Clin. Microbiol. 31:798–803.

    PubMed  Google Scholar 

  • van Belkum, A., M. Struelens, and W. Quint. 1993b. Typing of Legionella pneumophila strains by polymerase chain reaction-mediated DNA fingerprinting. J. Clin. Microbiol. 31:2198–2200.

    PubMed  Google Scholar 

  • van Belkum, A. 1994. DNA fingerprinting of medically important microorganisms by use of PCR. Clin. Microbiol. Rev. 7:174–184.

    PubMed  Google Scholar 

  • van Belkum, A., M. Sluijter, R. de Groot, H. Verbrugh, and P. W. M. Hermans. 1996. Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J. Clin. Microbiol. 34:1176–1179.

    PubMed  Google Scholar 

  • van Belkum, A., R. B. Navarro, and A.A.T. Vargas. 1994. Classification of the uptake hydrogenase-positive (Hup+) bean rhizobia as Rhizobium tropici. Appl. Environ. Microbiol. 60:554–5

    Google Scholar 

  • Vera Cruz, C. M., L. Halda, F. Louws, D. Z. Skinner, M. L. George, R. J. Nelson, F. J. de Bruijn, C. Rice, and J. E. Leach. 1995. Repetitive sequence-based PCR of Xanthomonas oryzae pv. oryzae and Pseudomonas species. Intl. Rice Res. Instit. Newsletter 20:23–25.

    Google Scholar 

  • 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 Research 19:6823–6831.

    Article  PubMed  CAS  Google Scholar 

  • Versalovic, J., V. Kapur, Jr. Mason, U. Shah, T. Koeuth, J. R. Lupski, and J. M. Musser. 1993. Penicillin resistant Streptococcus pneumoniae strains recovered in Houston, Texas: Identification and molecular characterization of multiple clones. J. Infect. Dis. 167:850–856.

    Article  PubMed  CAS  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. Meth. Mol. Cell Biol. 5:25–40.

    CAS  Google Scholar 

  • Versalovic, J., V. Kapur, T. Koeuth, G. H. Mazurek, T. S. Whittam, J. M. Musser, and J. R. Lupski. 1995. Automated DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction. Arch. Pathol. Lab. Med. 119:23–29.

    PubMed  CAS  Google Scholar 

  • Versalovic, J., and J. R. Lupski. 1995. DNA fingerprinting of Neisseria strains by rep-PCR. Meth. Mol. Cell Biol. 5:96–104.

    Google Scholar 

  • Versalovic, J., and J. R. Lupski. 1996. Distinguishing bacterial and fungal pathogens by repetitive sequence-based PCR (rep-PCR). LabMedica Intl. in press.

    Google Scholar 

  • Welsh, J., C. Pretzman, D. Postic, I. Saint Girons, G. Baranton, and M. McClelland. 1992. Genomic fingerprinting by arbitrarily primed polymerase chain reaction resolves Borrelia burgdorferi into three distinct phyletic groups. Int. J. Syst. Bacteriol. 42:370–377.

    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 

  • Wenzel, R. and R. Herrmann. 1988. Repetitive DNA sequences in Mycoplasma pneumoniae. Nucl. Acids Res. 16:8337–8350.

    Article  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 

  • Woods, C., J. Versalovic, T. Koeuth, and J. R. Lupski. 1993. Whole cell rep-PCR allows rapid assessment of clonal relationships of bacterial isolates. J. Clin. Microbiol. 31:1927–1931.

    PubMed  CAS  Google Scholar 

  • Woods, C. R., J. Versalovic, T. Koeuth, and J. R. Lupski. 1992. Analysis of relationships among isolates of Citrobacter diversus using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J. Clin. Microbiol. 30:2921–2929.

    PubMed  CAS  Google Scholar 

Download references

Authors
  1. James Versalovic
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Frans J. de Bruijn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James R. Lupski
    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

Versalovic, J., de Bruijn, F.J., Lupski, J.R. (1998). Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes. 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_34

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-6369-3_34

  • 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