Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling

FEMS Microbiology Letters

Volumn 160, Issue 1, 1998, Pages 145-150

  Van Doorn, Nathalie E M ^a   Namavar, Ferry ^a   Kusters, Johannes G ^a   Van Rees, Emmelien P ^a   Kuipers, Ernst J ^b   De Graaff, Johannes ^c  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Cluster analysis; Gastric disease; Genotyping; Helicobacter pylori

Indexed keywords

BACTERIAL DNA; REPETITIVE DNA;

ARTICLE; CLUSTER ANALYSIS; COMPUTER ANALYSIS; CONTROLLED STUDY; DNA FINGERPRINTING; HELICOBACTER PYLORI; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT; SYMPTOM;

DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; GASTRITIS; GENOME, BACTERIAL; GENOTYPE; HELICOBACTER PYLORI; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); HELICOBACTER PYLORI; NEGIBACTERIA; PROKARYOTA;

EID: 0032032896     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(98)00025-1     Document Type: Article

References (27)

1. Blaser, M.J. (1990) Heliobacter pylori and the pathogenesis of gastroduodenal inflammation. Clin. Infect. Dis. 15, 386-393.
2. Kuipers, E.J., Thijs, J.C. and Festen, H.P.M. (1995) The prevalence of Helicobacter pylori in peptic ulcer disease. Aliment. Pharmacol. Ther. 9, 59-69.
3. Kuipers, E.J. (1994) Infection with Helicobacter pylori. Section 1.4, Clinical Disease. In: IARC Monograph Vol. 61. Schistosomes, Liver Flukes and Helicobacter pylori. World Health Organization, International Agency for Research on Cancer, Lyon.
4. Parsonnet, J., Hansen, S., Rodriguez, S., Gelb, A.B., Warnke, R.A., Jellum, E., Orentreich, N., Vogelman, J.H. and Friedman, G.D. (1994) Helicobacter pylori infection and gastric lymphoma. N. Eng. J. Med. 330, 1267-1271.
5. Kung, J.S.L., Ho, B. and Chan, S.H. (1989) Biotyping of Campylobacter pylori. J. Med. Microbiol. 29, 203-206.
6. Go, M.F., Kapur, V., Graham, D.Y. and Musser, J.M. (1996) Population genetic analysis of Helicobacter pylori by multi locus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J. Bacteriol. 178, 3934-3938.
7. Simoons-Smit, I.M., Appelmelk, B.J., Verboom, T., Negrini, R., Penner, J.L., Aspinall, G.O., Moran, A.P., Fei Fei, S., Bi-Shan, S., Rudnica, W., Savio, A. and de Graaff, J. (1996) Typing of Helicobacter pylori with monoclonal antibodies against Lewis antigens in lipopolysaccharide. J. Clin. Microbiol. 34, 2196-2200.
8. Langenberg, W., Rauws, E.A.J., Widjojokusumo, A., Tytgat, G.N.J. and Zanen, H.C. (1986) Identification of Campylobacter pyloridis isolates by restriction endonuclease DNA analysis. J. Clin. Microbiol. 24, 414-417.
9. Majewski, S.I.H. and Goodwin, C.S. (1988) Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation. J. Infect. Dis. 3, 465-471.
10. Simor, A.E., Shames, B., Drumm, B., Sherman, P., Low, D.E. and Penner, J.L. (1990) Typing of Campylobacter pylori by bacterial DNA restriction endonuclease analysis and determination of plasmid profile. J. Clin. Microbiol. 28, 83-86.
11. Akopyanz, N., Bukanov, N.O., Westblom, T.U. and Berg, D.E. (1992) PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 20, 6221-6225.
12. Foxall, P.A., Hu, L. and Mobley, H.L.T. (1992) Use of polymerase chain reaction-amplified Helicobacter pylori urease structural genes for differentiation of isolates. J. Clin. Microbiol. 30, 739-741.
13. Hurtado, A., Owen, R.J. and Desai, M. (1994) Flagellin gene profiling of Helicobacter pylori infecting symptomatic and asymptomatic individuals. Res. Microbiol. 145, 585-594.
14. Morgan, D.D. and Owen, R.J. (1990) Use of DNA restriction endonuclease digest and ribosomal RNA gene probe patterns to fingerprint Helicobacter pylori and Helicobacter mustelae isolated from human and animal host. Mol. Cell. Probes 4, 321-334.
15. Taylor, D.E., Eaton, M., Chang, N. and Salama, S.M. (1992) Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level. J. Bacteriol. 174, 6800-6806.
16. Akopyanz, N., Bukanov, N.O., Westblom, T.U., Kresovich, S. and Berg, D.E. (1992) DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 20, 5137-5142.
17. Go, M.F., Chan, K.Y., Versalovic, J., Koeuth, T., Graham, D.Y. and Lupski, J.R. (1995) Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations. Scand. J. Gastroenterol. 30, 640-646.
18. Yoshimura, H.H., Evans, D.G. and Graham, D.Y. (1993) DNA-DNA hybridization demonstrates apparent genetic differences between Helicobacter pylori from patients with duodenal ulcer and asymptomatic gastritis. Dig. Dis. Sci. 38, 1128-1131.
19. Covacci, A., Censini, S., Bugnoli, M., Petracca, R., Burroni, D., Macchia, G., Massone, A., Pappini, A., Xiang, Z.Y., Figura, N. and Rappuoli, R. (1993) Molecular characterization of the 128-kDa immunodominant antigen of Helicobacter pylori associated with cytotoxicity and duodenal ulcer. Proc. Natl. Acad. Sci. USA 90, 5791-5795.
20. Xiang, Z., Bugnoli, M., Rappuoli, R., Covacci, A., Ponzetto, A. and Crabtree, J.E. (1993) Helicobacter pylori: host responses in peptic ulceration. Lancet 341, 900-901.
21. Van Steenbergen, T.J.M., Colloms. S.D., Hermans, P.W.M., de Graaff, J. and Plaster, R.H.A. (1995) Genomic DNA fingerprinting by restriction fragment end labeling. Proc. Natl. Acad. Sci. USA 92, 5572-5576.
22. Dent, J.C. and McNulty, C.A.M. (1988) Evaluation of a new selective medium for Campylobacter pylori. Eur. J. Clin. Microbiol. Infect. Dis. 7, 555-568.
23. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Smith, J.A., Seidman, J.G. and Struhl, K. (1987) In: Current Protocols in Molecular Biology. Greene Publishing Associates and Wiley-Interscience, New York.
24. Versovalic, J., Koeuth, T. and Lupski, J.R. (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19, 6823-6831.
25. Versovalic, J., Kapur, V., Mason, V.O. Jr., Shah, U., Koeuth, T., Lupski, J.R. and Musser, J.M. (1993) Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J. Infect. Dis. 167, 850-856.
26. Cobb, B.D. and Clarkson, J.M. (1994) A simple procedure for optimizing the polymerase chain reaction (PCR) using modified Taguchi methods. Nucleic Acids Res. 22, 3801-3805.
27. Michelli, M.R., Bova, R., Pascale, E. and D'Ambrosio, E. (1994) Reproducible DNA fingerprinting with the random amplified polymorphic DNA (RAPD) method. Nucleic Acids Res. 22, 1921-1922.