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Restriction Fragment End Labeling Analysis: High-Resolution Genomic Typing of Streptococcus pneumoniae Isolates

  • Peter W. M. Hermans
  • Marcel Sluijter
  • Alex van Belkum
Part of the Methods in Molecular Medicine™ book series (MIMM, volume 48)

Abstract

Streptococcus pneumoniae (pneumococcus) is one of the leading bacterial pathogens causing illness and death among young children, the elderly, and persons with certain underlying medical conditions (1). Pneumococci are often part of the normal nasopharyngeal flora, especially in young children. Pneumococcal colonization is an important risk factor: children colonized with S. pneumoniae more often develop acute otitis media than children who are not colonized (2-5).

Keywords

Acute Otitis Medium Unweighted Pair Group Method With Arithmetic Average Geiger Counter Underlying Medical Condition Actinobacillus Actinomycetemcomitans 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Centers for Diseases Control (1997) Prevention of pneumococcal disease-recommendation of the Advisory Committee on Immunization Practices (ACIP). MMWR 46, 1–24.Google Scholar
  2. 2.
    Zenni, M. K., Cheatham, S. H., Thompson, J. M., Reed, G. W., Batson, A. B., Palmer, P. S., Holland, K. L., and Edwards, K. M. (1995) Streptococcus pneumoniae colonization in the young child: association with otitis media and resistance to penicillin. J. Pediatr. 127, 533–537.PubMedCrossRefGoogle Scholar
  3. 3.
    Homoe, P., Prag, J., Farholt, S., Henrichsen, J., Hornsleth, A., Kilian, M., and Jensen, J. S. (1996) High rate of nasopharyngeal carriage of potential pathogens among children in Greenland: results of a clinical survey of middle-ear disease. Clin. Infect. Dis. 23, 1081–1090.PubMedGoogle Scholar
  4. 4.
    Faden, H., Duffy, L., Wasielewski, R., Wolf, J., Krystofik, D., and Tung, Y. (1997) Relationship between nasopharyngeal colonization and the development of otitis media in children. J. Infect. Dis. 175, 1440–1445.PubMedCrossRefGoogle Scholar
  5. 5.
    Sluijter, M., Faden, H., de Groot, R., Lemmens, N., Goessens, W. H. F., van Belkum, A., and Hermans, P. W. M. (1998) Molecular characterization of pneu mococcal nasopharynx isolates in children during the first two years of life. J. Clin. Microbiol. 36, 2248–2253.PubMedGoogle Scholar
  6. 6.
    Geslin, P., Buu-Hoi, A., Fremaux, A., and Acar, J. F. (1992) Antimicrobial resistance in Streptococcus pneumoniae: an epidemiology survey in France, 1970-1990. Clin. Infect. Dis. 15, 95–98.PubMedGoogle Scholar
  7. 7.
    Koornof, H. J., Wasas, A., and Klugman, K. P. (1992) Antimicrobial resistance in Streptococcus pneumoniae: a South African perspective. Clin. Infect. Dis. 15, 84–97.Google Scholar
  8. 8.
    Kristinsson, K. G., Hjalmardottir, M. A., and Steingrimsson, O. S. (1992) Increasing penicillin resistance in pneumococci in Iceland. Lancet 339, 1606–1607.PubMedCrossRefGoogle Scholar
  9. 9.
    Linares, J., Alonso, T., Perez, J. L., Ayats, J., Dominguez, M. A., Pallares, R., and Martin, R. (1992) Trends in antimicrobial resistance of clinical isolates of Streptococcus pneumoniae in Bellvitge Hospital, Barcelona, Spain (1979-1990). Clin. Infect. Dis. 15, 99–105.PubMedGoogle Scholar
  10. 10.
    Marton, A. (1992) Pneumococcal antimicrobial resistance: the problem in Hungary. Clin. Infect. Dis., 15, 106–111.PubMedGoogle Scholar
  11. 11.
    Centers for Diseases Control (1995) Emergence of penicillin-resistant Streptococcus pneumoniae-Southern Ontario, Canada. MMWR 44, 207–209.Google Scholar
  12. 12.
    Yoshida, R., Kaku, M., Kohno, S., Ishida, K., Mizukane, R., Takemura, H., Tanaka, H., Usui, T., Tomono, K., Koga, H., et al. (1995) Trends in antimicrobial resistance on Streptococcus pneumoniae in Japan. Antimicrob. Agents Chemother. 39, 1196–1198.PubMedGoogle Scholar
  13. 13.
    Dagan, R., Melamed, R., Muallem, M., Piglansky, L., and Yagupsky, P. (1996) Nasopharyngeal colonization in Southern Israel with antibiotic-resistant pneumococci during the first 2 years of life: relation to serotypes likely to be included in pneumococcal conjugate vaccines. J. Infect. Dis. 174, 1352–1355.PubMedGoogle Scholar
  14. 14.
    Soares, S., Kristinsson, K. G., Musser, J. M., and Tomasz, A. (1993) Evidence for the introduction of a multiresistant clone of serotype 6B Streptococcus pneumoniae from Spain to Iceland in the late 1980s. J. Infect. Dis. 168, 158–163.PubMedGoogle Scholar
  15. 15.
    Muñoz, R., Coffey, T. J., Daniels, M., Dowson, C. G., Laible, G., Casal, J., Hakenbeck, R., Jacobs, M., Musser, J. M., Spratt, B. G., and Tomasz, A. (1991) Intercontinental spread of a multiresistant clone of serotype 23F Streptococcus pneumoniae. J. Infect. Dis. 164, 302–306.PubMedGoogle Scholar
  16. 16.
    McDougal, L. K., Facklam, R. R., Reeves, M., Hunter, S., Swenson, J. M., Hill, B. C., and Tenover, F. C. (1992) Analysis of multiply antimicrobial-resistant isolates of Streptococcus pneumoniae from the United States. Antimicrob. Agents Chemother. 36, 2176–2184.PubMedGoogle Scholar
  17. 17.
    Gasc, A. M., Geslin, P., and Sicard, A. M. (1995) Relatedness of penicillin-resistant Streptococcus pneumoniae serogroup 9 strains from France and Spain. Microbiology 141, 623–627.PubMedCrossRefGoogle Scholar
  18. 18.
    Reichmann, P., Varon, E., Günther, E., Reinert, R. R., Lüttiken, R., Marton, A., Geslin, P., Wagner, J., and Hakenbeck, R. (1995) Penicillin-resistant Streptococcus pneumoniae in Germany: genetic relationship to clones from other European countries. J. Med. Microbiol. 43, 377–385.PubMedCrossRefGoogle Scholar
  19. 19.
    Hermans, P. W. M., Sluijter, M., Dejsirilert, S., Lemmens, N., Elzenaar, K., van Veen, A., Goessens, W. H. F., and de Groot, R. (1997) Molecular epidemiology of drug-resistant pneumococci: toward an international approach. Microb. Drug Resist. 3, 243–251.PubMedCrossRefGoogle Scholar
  20. 20.
    Coffey, T. J., Berron, S., Daniels, M., Garcia-Leoni, E., Cercenado, E., Bouza, E., Fenoll, A., and Spratt, B. G. (1996) Multiply antibiotic-resistant Streptococcus pneumoniae recovered from Spanish hospitals (1988-1994): Novel major clones of serotypes 14, 19F and 15F. Microbiology 142, 2747–2757.PubMedCrossRefGoogle Scholar
  21. 21.
    Smith, A. M. and Klugman, K. P. (1997) Three predominant clones identified within penicillin-resistant South-African isolates of Streptococcus pneumoniae. Microb. Drug Resist. 3, 385–389.PubMedCrossRefGoogle Scholar
  22. 22.
    Yoshida, R., Hirakata, Y., Kaku, M., Takemura, H., Tanaka, H., Tomono, K., Koga, H., Kohno, S., and Kamahira, S. (1997) Genetic relationship of penicillin resistant Streptococcus pneumoniae serotype19B strains in Japan. Epidemiol. Infect. 118, 105–110.PubMedCrossRefGoogle Scholar
  23. 23.
    Lund, E. and Henrichsen, J. (1978) Laboratory diagnosis, serology and epidemiology of Streptococcus pneumoniae, in Methods in Microbiology, vol. 12 (Bergan, T. and Norris, J. R., eds.), Academic Press, New York, pp. 241–262.Google Scholar
  24. 24.
    Nielsen, S. V. and Henrichsen, J. (1993) Capsular types and susceptibility to penicillin of pneumococci isolated from cerebrospinal fluid or blood in Denmark, 1983-1988. Scand J. Infect. Dis. 25, 165–170.PubMedCrossRefGoogle Scholar
  25. 25.
    Sessegolo, J. F., Levin, A. S. S., Levy, C. E., Asensi, M., Facklam, R. R., and Teixeira, L. M. (1994) distribution of serotypes and antimicrobial resistance of streptococcus pneumonia strains isolated in brazil from 1988 to 1992. J. Clin. Microbiol. 32, 906–911.PubMedGoogle Scholar
  26. 26.
    Shapiro, E. D. and Austrian, R. (1994) Serotypes responsible for invasive Streptococcus pneumoniaes infections among children in Connecticut. J. Infect. Dis. 169, 212–214.PubMedGoogle Scholar
  27. 27.
    Munoz, R., Musser, J. M., Crain, M., Briles, D. E., Marton, A., Parkinson, A. J., Sorensen, U., and Tomasz, A. (1992) Geographic distribution of penicillin-resistant clones of Streptococcus pneumoniae: characterization by penicillin-binding protein profile, surface protein A typing, and multilocus enzyme analysis. Clin. Infect. Dis. 15, 112–118.PubMedGoogle Scholar
  28. 28.
    Kell, C. M., Jordens, J. Z., Daniels, M., Coffey, T. J., Bates, J., Paul, J., Gilks, C., and Spratt, B. G. (1993) Molecular epidemiology of penicillin-resistant pneumococci isolated in Nairobi, Kenya. Infect. Immun. 61, 4382–4391.PubMedGoogle Scholar
  29. 29.
    Cherian, T., Steinhoff, M. C., Harrison, L. H., Rohn, D., McDougal, L. K., and Dick, J. (1994) A cluster of invasive pneumococcal disease in young children in child care. JAMA 271, 695–697.PubMedCrossRefGoogle Scholar
  30. 30.
    Munoz, R., Dowson, C. G., Daniels, M., Coffey, T. J., Martin, C., Hakenbeck, R., and Spratt, B. G. (1992) Genetics of resistance to third-generation cephalosporins in clinical isolates of Streptococcus pneumoniae. Mol. Microbiol. 6, 2461–2465.PubMedCrossRefGoogle Scholar
  31. 31.
    Smith, A. M., Klugman, K. P., Coffey, T. J., and Spratt, B. G. (1993) Genetic diversity of penicillin-binding protein 2B and 2X genes from Streptococcus pneumoniae in South Africa. Antimicrob. Agents Chemother. 37, 1938–1944.PubMedGoogle Scholar
  32. 32.
    Lefevre, J. C., Faucon, G., Sicard, A. M., and Gasc, A. M. (1993) DNA fingerprinting of Streptococcus pneumoniae strains by pulsed-field gel electrophoresis. J. Clin. Microbiol. 31, 2724–2728.PubMedGoogle Scholar
  33. 33.
    Hermans, P. W. M., Sluijter, M., Hoogenboezem, T., Heersma, H., van Belkum, A., and de Groot, R. (1995) Comparative study of five different DNA fingerprint techniques for molecular typing of Streptococcus pneumoniae strains. J. Clin. Microbiol. 33, 1606–1612.PubMedGoogle Scholar
  34. 34.
    Martin, B., Humbert, O., Camara, M., Guenzi, E., Walker, J., Mitchell, T., Andrew, P., Prudhomme, M., Alloing, G., Hakenbeck, R., Morrison, D. A., Boulnois, G. J., and Claverys, J.-P. (1992) A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniaes. Nucleic Acids Res. 20, 3479–3483.PubMedCrossRefGoogle Scholar
  35. 35.
    Versalovic, J., Koeuth, T., and Lupski, J. R. (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting bacterial genomes. Nucleic Acids Res. 19, 6823–6831.PubMedCrossRefGoogle Scholar
  36. 36.
    Van Belkum, A., Sluijter, M., de Groot, R., Verbrugh, H. A., and Hermans, P. W. M. (1996) A novel BOX-repeat PCR assay for high resolution typing of Streptococcus pneumoniae strains. J. Clin. Microbiol. 34, 1176–1179.PubMedGoogle Scholar
  37. 37.
    Van Steenbergen, T. J. M., Colloms, S. D., Hermans, P. W. M., de Graaff, J., and Plasterk, R. H. A. (1995) Genomic DNA fingerprinting by restriction fragment end labeling. Proc. Natl. Acad. Sci. USA 92, 5572–5576.PubMedCrossRefGoogle Scholar
  38. 38.
    Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.Google Scholar
  39. 39.
    Debets-Ossenkopp, Y. J., Sparrius, M., Kusters, J. G., Kolkman, J. J., and Vandenbroucke-Grauls, C. M. (1996) Mechanism of clarithromycin resistance in clinical isolates of Helicobacter pylori. FEMS Microbiol. Lett. 142, 37–42.PubMedCrossRefGoogle Scholar
  40. 40.
    Van Doorn, N. E., Namavar, F., Kusters, J. G., van Rees, E. P., Kuipers, E. J., and de Graaff, J. (1998) Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling. FEMS Microbiol. Lett. 160, 145–150.PubMedCrossRefGoogle Scholar
  41. 41.
    Kremer, K., van Soolingen, D., Frothingham, R., Haas, W. H., Hermans, P. W. M., Martin, C., Palittapongarnpim, P., Plikaytis, B. B., Riley, L. W., Yakrus, M. A., Musser, J. M., and van Embden, J. D. A. (1999) Comparison of molecular epidemiologic markers for Mycobacterium tuberculosis complex: an interlaboratory study on differentiation and reproducibility. J Clin Microbiol. (In Press).Google Scholar

Copyright information

© The Humana Press Inc., Totowa, NJ 2001

Authors and Affiliations

  • Peter W. M. Hermans
    • 1
  • Marcel Sluijter
    • 1
  • Alex van Belkum
    • 2
  1. 1.Department of PaediatricsErasmus University Medical Center RotterdamRotterdamdamThe Netherlands
  2. 2.Department of Medical Microbiology and Infectious DiseasesErasmus University Medical Center RotterdamRotterdamThe Netherlands

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