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DNA Fingerprinting of Prokaryotic Genomes

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DNA Profiling and DNA Fingerprinting

Part of the book series: Methods and Tools in Biosciences and Medicine ((MTBM))

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Abstract

DNA fingerprinting has become such an established technology that it has featured frequently in the media and is quite well known to the general public. This is largely a result of publicity surrounding a small number of high-profile criminal or litiginous cases. What is perhaps less well known is that the technology can also be applied to the study of prokaryotic organisms, where it has many uses. These uses may be either simple or complex, and the exact technology to be used will depend largely on the question to be asked or the hypothesis to be tested. Some of the simple uses for genotyping of prokaryotes in the laboratory would be to test for contamination of cultures or alterations in strain genotype during culture or manipulation. Further uses may concern the ecology or taxonomy of prokaryotic organisms, or applications to agricultural, veterinary or medical problems. In the latter cases, it may be to determine whether a patient (animal or human) is afflicted by a mixed or single infection of any given pathogen. Many additional questions can be asked concerning the disease under investigation. Specifically, routes of transmission and index cases can be sought, outbreaks can be investigated and disease dynamics fol lowed in a broader context. These last few are examples of the new science of molecular epidemiology, a marriage between traditional epidemiology and molecular biology.

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References

  1. Supply P, Magdalena J, Himpers S, Locht C (1997) Identification of novel inter-genic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 26:991–1003

    Article  PubMed  CAS  Google Scholar 

  2. Van Embden JDA, Cave DM, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM et al (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting. J Clin Microbiol 31: 406–409

    PubMed  Google Scholar 

  3. Leonard C, Chen Y, Mahillon J (1997) Diversity and differential distribution of IS231, IS232 and IS240 among Bacillus cereus, Bacillus thuringiensis and Bacillus mycoides. Microbiology 143: 2537–2547

    Article  PubMed  CAS  Google Scholar 

  4. Goyal M, Saunders NA, van Embden JDA, Young DB, Shaw RJ (1997) Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism. J Clin Microbiol 35: 647–651

    PubMed  CAS  Google Scholar 

  5. Korolik V, Moorthy L, Coloe PJ (1995) Differentiation of Campylobacter jejuni and Campylobacter coli strains by using restriction endonuclease DNA profiles and DNA fragment polymorphisms. J Clin Microbiol 33:1136–1140

    PubMed  CAS  Google Scholar 

  6. Saunders KE, McGovern KJ, Fox JG (1997) Use of pulsed-field gel electrophoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations. J Clin Microbiol 35: 2859–2863

    PubMed  CAS  Google Scholar 

  7. Fulton TR, Losada MC, Fluder EM, Chou GT (1995) rRNA operon restriction derived taxa for Streptomyces (RaDiTS). FEMS Microbiol Lett 125:149–158

    Article  PubMed  CAS  Google Scholar 

  8. Lhopital S, Bonacorsie S, Meis D, Brahimi N, Mathy S, Navarro J, Aigrain Y, Bingen E (1997) Molecular markers for differentiation of multiresistant Klebsiella pneumoniae isolates in a pediatric hospital. Infect Control Hosp Epidemiol 18: 743–748

    Article  PubMed  CAS  Google Scholar 

  9. Bingen EH, Desjardins P, Arlet G, Bourgeois F, Mariani-Kurkdjian P, Lambert-Zechovsky NY, Denamur E, Philippon A, Elion J (1993) Molecular epidemiology of plasmid spread among extended broadspectrum (-Lactamase-producing Klebsiella pneumoniae isolates in a pediatric hospital. J Clin Microbiol 31:179–184

    PubMed  CAS  Google Scholar 

  10. Van Belkum A, van Leeuwen W, Kluytmans J, Verbrugh H (1995) Molecular nosocomial epidemiology: high speed typing of microbial pathogens by arbitrary primed polymerase chain reaction assays. Infect Control Hosp Epidemiol 16: 658–666

    Article  PubMed  Google Scholar 

  11. Iriarte MP, Own RJ (1996) Repetitive and arbitrary primer DNA sequences in PCR-mediated fingerprinting of outbreak and sporadic isolates of Campylobacter jejuni. FEMS Immunol Med Microbiol 15: 17–22

    Article  PubMed  CAS  Google Scholar 

  12. Lam KM, Yamamoto R, DaMassa AJ (1995) DNA diversity among isolates of Campylobacter jejuni detected by PCR-based RAPD fingerprinting. Vet Microbiol 45:269–274

    Article  PubMed  CAS  Google Scholar 

  13. Gao Z, Jackson KM, Leslie DE (1996) Pitfalls in the use of random amplified polymorphic DNA (RAPD) for fingerprinting of gram negative organisms. Pathology 28: 173–177

    Article  PubMed  CAS  Google Scholar 

  14. Linton CJ, Jalal H, Leeming JP, Millar MR (1994) Rapid discrimination of Mycobacterium tuberculosis strains by random amplified polymorphic DNA analysis. J Clin Microbiol 32: 2169–2174

    PubMed  CAS  Google Scholar 

  15. Owen RJ, Bickley J, Hurtado A, Fraser A, Pounder RE (1994) Comparison of PCR-based restriction length polymorphism analysis of urease genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy. J Clin Microbiol 32: 1203–1210

    PubMed  CAS  Google Scholar 

  16. Owen RJ, Fitzgerald C, Sutherland K, Borman P (1994) Flagellin gene polymorphism analysis of Campylobacter jejuni infecting man and other hosts and comparison with biotyping and somatic antigen serotyping. Epidemiol Infect 113: 221–234

    Article  PubMed  CAS  Google Scholar 

  17. Jersek B, Tcherneva E, Rijpens N, Herman L (1996) Repetitive element sequence-based PCR for species and strain discrimination in the genus Listeria Lett Appl Microbiol 23: 55–60

    Article  CAS  Google Scholar 

  18. Marshall DG, Coleman DC, Sullivan DJ, Xia H, O’Morain CA, Smyth CJ (1996) Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive sequences. J Appl Bacteriol 81: 509–517

    PubMed  CAS  Google Scholar 

  19. Rychlik I, Bejckova L (1994) Oligonucleotide (GTG)5 in bacterial DNA fingerprinting. Vet Med Praha 39: 567–578

    PubMed  CAS  Google Scholar 

  20. Cilliers FJ, Warren RM, Hauman JH, Wiid IJF, van Helden PD (1997) Oligonucleotide (GTG)5 as an epidemiological tool in the study of nontuberculous mycobacteria. J Clin Microbiol 35: 1545–1549

    PubMed  CAS  Google Scholar 

  21. Wiid IJF, Werely C, Beyers N, Donald P, van Helden PD (1994) Oligonucleotide (GTG)5 as a marker for Mycobacterium tuberculosis strain identification. J Clin Microbiol 32:1318–1321

    PubMed  CAS  Google Scholar 

  22. Kaufhold A, Podbielski A, Baumgarten G, Blokpoel M, Top J, Schouls L (1994) Rapid typing of group A streptococci by the use of DNA amplification and nonradioactive allele specific oligonucleotide probes. FEMS Microbiol Lett 119:19–26

    Article  PubMed  CAS  Google Scholar 

  23. Salazar NM, Caetano-Anolles G (1996) Nucleic acid scanning-by-hybridization of enterohemorrhagic Escherichia coli isolates using oligodeoxynucleotide arrays. Nucleic Acids Res 15: 5056–5057

    Article  Google Scholar 

  24. Mazurier S, van de Giessen A, Heuvelman K, Wernars K (1992) RAPD analysis of Campylobacter isolates: DNA fingerprinting without the need to purify DNA. Lett Appl Microbiol 14: 260–262

    Article  PubMed  CAS  Google Scholar 

  25. Woods CR, Versalovic J, Koeuth T, Lupski JR (1993) Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J Clin Microbiol 31:1927–1931

    PubMed  CAS  Google Scholar 

  26. Victor T, du Toit R, van Helden PD (1992) Purification of sputum samples through sucrose improves the detection of Mycobacterium tuberculosis by PCR. J Clin Microbiol 30: 1514–1517

    PubMed  CAS  Google Scholar 

  27. Southern EM (1975) Detection of specific sequences among DNA fragments by gel electrophoresis. J Mol Biol 98: 503–515

    Article  PubMed  CAS  Google Scholar 

  28. Epplen C, Santos EJM, Mäueler W, van Helden PD, Epplen JT (1997) On simple repetitive DNA sequences and complex diseases. Electrophoresis 18:1577–1585

    Article  PubMed  CAS  Google Scholar 

  29. Rudi P, Kolb C, Maiwald M, Kuck D, Sieg A, Galle PR, Stremmel W (1998) Diversity of Helicobacter pylor vacA and cagA genes and relationship to vacA and cagA protein expression, cytotoxin production and associated diseases. J Clin Microbiol 36: 944–948

    PubMed  CAS  Google Scholar 

  30. Frothingham R, Meeker-O’Connell WA (1998) Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144:1189–1196

    Article  PubMed  CAS  Google Scholar 

  31. Bachellier S, Clement JM, Hofnung M, Gilson E (1997) Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145: 551–562

    PubMed  CAS  Google Scholar 

  32. Tyler KD, Wang G, Tyler SD, Johnson WM (1997) Factors affecting reliability and reproducibility of amplificationbased DNA fingerprinting of representative bacterial pathogens. J Clin Microbiol 35: 339–346

    PubMed  CAS  Google Scholar 

  33. Haas WH, Butler WR, Woodley CL, Crawford JT (1993) Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex. J Clin Microbiol 31:1293–1298

    PubMed  CAS  Google Scholar 

  34. Riipkema SG, Molkenboer MJ, Schouls LM, Jongejan F, Schellekens JF (1995) Simultaneous detection and genotyping of three genomic groups of Borrelia burgdorferi sensu lato in Dutch Ixodes ricinus ticks by characterization of the amplified intergenic spacer region between 5S and 23S rRNA genes. J Clin Microbiol 33:3091–3095

    Google Scholar 

  35. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M et al (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907–914

    PubMed  CAS  Google Scholar 

  36. Van Soolingen D, de Haas PE, Blumenthal RM, Kremer K, Sluejter M, Pijnenburg JE, Schouls LM, Thole JE, Dessens-Kroon MW, van Embden JD (1996) Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis. J Bacterial 178:78–84

    Article  Google Scholar 

  37. Owen RJ, Bickley J, Hurtado A, Fraser A, Pounder RE (1994) Comparison of PCR-based restriction lenth polymorphism analysis of urease genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy. J Clin Microbiol 32:1203–1210

    PubMed  CAS  Google Scholar 

  38. Seward RJ, Ehrenstein B, Grundmann HJ, Towner KJ (1997) Direct comparison of two commercially available computer programs for analysing DNA fingerprinting gels. J Med Microbiol 46: 314–320

    Article  PubMed  CAS  Google Scholar 

  39. Warren R, Richardson J, Sampson S, Hauman J, Beyers N, Donald P, van Helden PD (1996) Genotyping of M. tuberculosis with additional markers enhances accuracy in epidemiological studies. J Clin Microbiol 34: 2219–2224

    PubMed  CAS  Google Scholar 

  40. Small PM, Hopewell PC, Singh SP, Paz A, Porsomet J, Ruston DC, Schecter GF, Daley CL, Schoolnik GK (1994) The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N Engl J Med 330: 1703–1709

    Article  PubMed  CAS  Google Scholar 

  41. Vaneechoutte M (1996) DNA fingerprinting techniques for microorganisms. A proposal for classification and nomenclature. Mol Biotechnol 6: 115–142

    Article  PubMed  CAS  Google Scholar 

  42. Warren R, Hauman J, Beyers N, Richardson M, Schaaf HS, Donald P, van Helden P (1996) Unexpectedly high strain diversity of Mycobacterium tuberculosis in a high-incidence community. SA Med J 86: 45–49

    CAS  Google Scholar 

  43. Van Soolingen D, Qian L, de Haas P, Douglas J, Taore H, Portaels F, Qing H, Enkhsaikan D, Nymadowa P, van Embden J (1995) Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J Clin Microbiol 33:3234–3238

    PubMed  Google Scholar 

  44. Hermans PWM, Messadi F, Guybrexabher H, van Soolingen D, de Haas P, Heersma H, de Neeling H, Ayoub A, Portaels F, Frommel D et al (1995) Analysis of the population structure of Mycobacterium tuberculosis in Ethiopia, Tunisia and the Netherlands: usefulness of DNA typing for global tuberculosis epidemiology. J Infect Dis 171:1504–1513

    Article  PubMed  CAS  Google Scholar 

  45. Yurieva O, Kholodii G, Minakhin L, Gorlenko Z, Kalyaeva E, Mindlin S, Nikoforov V (1997) Intercontinental spread of promiscuous mercury-resistance transposons in environmental bacteria. Mol Microbiol 24:321–329

    Article  PubMed  CAS  Google Scholar 

  46. Blower SM, Small PM, Hopewell PC (1996) Control strategies for tuberculosis epidemics: new models for old problems. Science 273: 497–500

    Article  PubMed  CAS  Google Scholar 

  47. Bourgoin F, Guedon G, Pebay M, Roussel Y, Panis C, Decaris B (1996) Characterization of a mosaic ISS1 element and evidence for the recent horizontal transfer of two different types of ISS1 between Streptococcus thermophilus and Lactococcus lactis. Gene 178:15–23

    Article  PubMed  CAS  Google Scholar 

  48. Gupta S, Ferguson N, Anderson R (1998) Chaos, persistence and evolution of strain structure in antigenically diverse infectious agents. Science 280: 912–915

    Article  PubMed  CAS  Google Scholar 

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© 1999 Birkhäuser Verlag

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van Helden, P.D. (1999). DNA Fingerprinting of Prokaryotic Genomes. In: Epplen, J.T., Lubjuhn, T. (eds) DNA Profiling and DNA Fingerprinting. Methods and Tools in Biosciences and Medicine. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-7582-0_1

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  • DOI: https://doi.org/10.1007/978-3-0348-7582-0_1

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-7643-6018-4

  • Online ISBN: 978-3-0348-7582-0

  • eBook Packages: Springer Book Archive

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