Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: Experimental results and meta-analysis

Journal of Clinical Microbiology

Volumn 37, Issue 12, 1999, Pages 4071-4080

  Burucoa, Christophe ^a   Lhomme, Vincent ^a   Fauchere, Jean Louis ^a  

^a POITIERS UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; DIAGNOSTIC ACCURACY; DNA FINGERPRINTING; GENOTYPE; HELICOBACTER PYLORI; META ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA (MICROORGANISMS); HELICOBACTER PYLORI; NEGIBACTERIA;

EID: 0032728091     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.37.12.4071-4080.1999     Document Type: Article

References (76)

1. Akashi, H., T. Hayashi, H. Koizuka, T. Shimoyama, and T. Tamura. 1996. Strain differentiation and phylogenic relationships, in terms of base sequence of the ureB gene, of Helicobacter pylori. J. Gastroenterol. 31(Suppl. 9):16-23.
2. Akopyants, N. S., K. A. Eaton, and D. E. Berg. 1995. Adaptative mutation and cocolonization during Helicobacter pylori infection of gnotobiotic piglets. Infect. Immun. 63:116-121.
3. Akopyanz, N., N. O. Bukanov, T. U. Westblom, S. Kresovich, and D. E. Berg. 1992. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 20:5137-5142.
4. Akopyanz, N., N. O. Bukanov, T. U. Westblom, and D. E. Berg. 1992. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 20:6221-6225.
5. Bamford, K. B., J. Bickley, J. S. A. Collins, B. T. Johnston, S. Potts, V. Boston, R. J. Owen, and J. M. Sloan. 1993. Helicobacter pylori: comparison of DNA fingerprints provides evidence for intrafamilial infection. Gut 34:1348-1350.
6. Beji, A., P. Vincent, I. Darchis, M. O. Husson, A. Cortot, and H. Leclerc. 1989. Evidence of gastritis with several Helicobacter pylori strains. Lancet i: 1402-1403.
7. Cho, M.-J., W.-K. Lee, Y.-S. Jeon, K.-H. Kim, S.-H. Kim, S.-C. Bai, K.-H. Rhee, Y.-O. Kim, H.-S. Yoon, and N.-S. Kim. 1995. Intrafamilial transmission of Helicobacter pylori detected by random amplified polymorphic DNA fingerprinting. Mol. Cells 5:508-513.
8. Clayton, C. L., H. Kleanthous, J. C. Dent, C. A. M. McNulty, and S. Tabaqchali. 1991. Evaluation of fingerprinting methods for identification of Helicobacter pylori strains. Eur. J. Clin. Microbiol. Infect. Dis. 10:1040-1047.
9. Clayton, C. L., H. Kleanthous, D. D. Morgan, L. Puckey, and S. Tabaqchali. 1993. Rapid fingerprinting of Helicobacter pylori by polymerase chain reaction and restriction fragment length polymorphism analysis. J. Clin. Microbiol. 31:1420-1425.
10. Davin-Regli, A., Y. Abed, R. N. Charrel, C. Bollet, and P. de Micco. 1995. Variations in DNA concentrations significantly affect the reproducibility of RAPD fingerprint patterns. Res. Microbiol. 146:561-568.
11. Desai, M., D. Linton, R. J. Owen, H. Cameron, and J. Stanley. 1993. Genetic diversity of Helicobacter pylori indexed with respect to clinical symptomatology, using a 16S rRNA and a species-specific DNA probe. J. Appl. Bacteriol. 75:574-582.
12. Desai, M., D. Linton, R. J. Owen, and J. Stanley. 1994. Molecular typing of Helicobacter pylori isolates from asymptomatic, ulcer and gastritis patients by urease gene polymorphism. Epidemiol. Infect. 112:151-160.
13. Dore, M. P. M. S. Osato, D. H. Kwon, D. Y. Graham, and F. A. K. El-Zaatari. 1998. Demonstration of unexpected antibiotic resistance of geno-typically identical Helicobacter pylori isolates. Clin. Infect. Dis. 27:84-89.
14. Dubois, A., D. E. Berg, E. T. Incecik, N. Fiala, L. M. Heman-Ackah, G. I. Perez-Perez, and M. J. Blaser. 1996. Transient and persistent experimental infection of nonhuman primates with Helicobacter pylori: implications for human disease. Infect. Immun. 64:2885-2891.
15. Dunn, B. E., H. Cohen, and M. J. Blaser. 1997. Helicobacter pylori. Clin. Infect. Dis. 10:720-741.
16. Dzierzanowska, D., A. Gzyl, E. Rozynek, E. Augustynowicz, U. Wojda, D. Celinska-Cedro, M. Sankowska, and T. Wadström. 1996. PCR for identifi cation and typing of Helicobacter pylori isolated from children. J. Physiol. Pharmacol. 47:101-114.
17. The EUROGAST Study Group. 1993. An international association between Helicobacter infection and gastric cancer. Lancet 341:1359-1362.
18. Evans, D. G., D. J. Evans, H. C. Lampert, and D. Y. Graham. 1995. Restriction fragment length polymorphism in the adhesin gene hpaA of Helicobacterpylori. Am. J. Gastroenterol. 90:1282-1288.
19. Forbes, K. J., Z. Fang, and T. H. Pennington. 1995. Allelic variation in the Helicobacter pylori flagellin genes flaA and flaB: its consequences for straintyping schemes and population structure. Epidemiol. Infect. 114:257-266.
20. Foxall, P. A., L.-T. Hu, and H. L. T. Mobley. 1992. Use of polymerase chain reaction-amplified Helicobacter pylori urease structural genes for differentiation of isolates. J. Clin. Microbiol. 30:739-741.
21. Fraser, A. G., J. Bickley, R. J. Owen, and R. E. Pounder. 1992. DNA fingerprints of Helicobacter pylori before and after treatment with omepra zole. J. Clin. Pathol. 45:1062-1065.
22. Fujimoto, S., B. Marshall, and M. J. Blaser. 1994. PCR-based restriction fragment length polymorphism typing of Helicobacter pylori. J. Clin. Microbiol. 32:331-334.
23. Ge, Z., and D. E. Taylor. 1998. Helicobacter pylori - molecular genetics and diagnostic typing. Br. Med. Bull. 54:31-38.
24. Georgopoulos, S. D., A. F. Mentis, C. A. Spiliadis, L. S. Tzouvelekis, E. Tzelepi, A. Moshopoulos, and N. Skandalis. 1996. Helicobacter pylori infection in spouses of patients with duodenal ulcers and comparison of ribosomal RNA gene patterns. Gut 39:634-638.
25. Go, M. F., K. Y. Chan, J. Versalovic, T. Koeuth, D. Y. Graham, and J. R. Lupski. 1995. Cluster analysis of Helicobacter pylori genomic DNA finger prints suggests gastroduodenal disease-specific associations. Scand. J. Gastroenterol. 30:640-646.
26. Graham, D. Y., and M. F. Go. 1993. Helicobacter pylori: current status. Gastroenterology 105:279-282.
27. Hirschl, A. M., M. Richter, A. Makristathis, P. M. Prückl, B. Willinger, K. Schütze, and M. L. Rotter. 1994. Single and multiple strain colonization in patients with Helicobacter pylori-associated gastritis: detection by macrorestriction DNA analysis. J. Infect. Dis. 170:473-475.
28. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discrimina tory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-2466.
29. Hurtado, A., and R. J. Owen. 1994. Identification of mixed genotypes in Helicobacter pylori from gastric biopsy tissue by analysis of urease gene polymorphisms. FEMS Immunol. Med. Microbiol. 8:307-313.
30. Hurtado, A., R. J. Owen, and M. Desai. 1994. Flagellin gene profiling of Helicobacter pylori infecting symptomatic and asymptomatic individuals. Res. Microbiol. 145:585-594.
31. Ito, A., T. Fujioka, T. Kubota, and M. Nasu. 1996. Molecular typing of Helicobacter pylori: differences in pathogenicity among diverse strains. J. Gastroenterol. 31:1-5.
32. Jorgensen, M., G. Daskalopoulos, V. Warburton, H. M. Mitchell, and S. L. Hazell. 1996. Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: identification from sequential and multiple biopsy specimens. J. Infect. Dis. 174:631-635.
33. Kansau, I., J. Raymond, E. Bingen, P. Courcoux, N. Kalach, M. Bergeret, N. Braimi, C. Dupont, and A. Labigne. 1996. Genotyping of Helicobacter pyloriisolates by sequencing of PCR products and comparison with the RAPD technique. Res. Microbiol. 147:661-669.
34. Labigne, A., V. Cussac, and P. Courcoux. 1991. Shuttle cloning and nucleotide sequences of Helicobacter pylori genes responsible for urease activity. J. Bacteriol. 173:1920-1931.
35. Li, C., D. A. Ferguson, T. Ha, D. S. Chi, and E. Thomas. 1993. A highly specific and sensitive DNA probe derived from chromosomal DNA of Helicobacter pylori is useful for typing H. pylori isolates. J. Clin. Microbiol. 31: 2157-2162.
36. Li, C., T. Ha, D. S. Chi, D. A. Ferguson, C. Jiang, J. J. Laffan, and E. Thomas. 1997. Differentiation of Helicobacter pylori strains directly from gastric biopsy specimens by PCR-based restriction fragment length polymor phism analysis without culture. J. Clin. Microbiol. 35:3021-3025.
37. Linton, D., M. Moreno, R. J. Owen, and J. Stanley. 1992. 16S rrn gene copy number in Helicobacter pylori and its application to molecular typing. J. Appl. Bacteriol. 73:501-506.
38. Majewski, S. I. H., and C. S. Goodwin. 1988. Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation. J. Infect. Dis. 157:465-471.
39. Marshall, D. G., A. Chua, P. W. Keeling, D. J. Sullivan, D. C. Coleman, and C. J. Smyth. 1995. Molecular analysis of Helicobacter pylori populations in antral biopsies from individual patients using randomly amplified polymor phic DNA (RAPD) fingerprinting. FEMS Immunol. Med. Microbiol. 10: 317-323.
40. Marshall, D. G., D. C. Coleman, D. J. Sulivan, H. Xia, C. A. O'Morain, and C. J. Smyth. 1996. Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive sequences. J. Appl. Bacteriol. 81:509-517.
41. Meunier, J. R., and P. A. D. Grimont. 1993. Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. Res. Microbiol. 144: 373-379.
42. Moore, R. A., A. Kureishi, S. Wong, and L. E. Bryan. 1993. Categorization of clinical isolates of Helicobacter pylori on the basis of restriction digest analyses of polymerase chain reaction-amplified ureC genes. J. Clin. Microbiol. 31:1334-1335.
43. Morgan, D. D., and R. J. Owen. 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 hosts. Mol. Cell. Probes 4:321-334.
44. Nwokolo, C. H., J. Bickley, A. R. Attard, R. J. Owen, M. Costas, and I. A. Fraser. 1992. Evidence of clonal variants of Helicobacter pylori in three generations of a duodenal ulcer disease family. Gut 33:1323-1327.
45. Ohta-Tada, U., A. Takagi, Y. Koga, S. Kamiya, and T. Miwa. 1997 Flagellin gene diversity among Helicobacter pylori strains and IL-8 secretion from gastric epithelial cells. Scand. J. Gastroenterol. 32:455-459.
46. Owen, R. J., J. Fraser, M. Costas, D. Morgan, and D. R. Morgan. 1990. Signature patterns of DNA restriction fragments of Helicobacter pylori be fore and after treatment. J. Clin. Pathol. 43:646-649.
47. Owen, R. J., J. Bickley, M. Costas, and D. R. Morgan. 1991. Genomic variation in Helicobacter pylori: application to identification of strains. Scand, J. Gastroenterol. Suppl. 181:43-50.
48. Owen, R. J., J. Bickley, A. Lastovica, J. P. Dunn, P. Borman, and C. Hunton. 1992. Ribosomal RNA gene patterns of Helicobacter pylori from surgical patients with healed and recurrent peptic ulcers. Epidemiol. Infect. 108: 39-50.
49. Owen, R. J., C. Hunton, J. Bickley, M. Moreno, and D. Linton. 1992. Ribosomal RNA gene restriction patterns of Helicobacter pylori: analysis and appraisal of HaeIII digests as a molecular typing system. Epidemiol. Infect. 109:35-47.
50. Owen, R. J., G. D. Bell, M. Desai, M. Moreno, P. W. Gant, P. H. Jones, and D. Linton. 1993. Biotype and molecular fingerprints of metronidazole-resis tant strains of Helicobacter pylori from antral gastric mucosa. J. Med. Microbiol. 38:5-12.
51. Owen, R. J., M. Desai, N. Figura, P. F. Bayeli, L. Di Gregorio, M. Russi, and R. A. Musmanno. 1993. Comparisons between degree of histological gastritis and DNA fingerprints, cytotoxicity and adhesivity of Helicobacter pylori from different gastric sites. Eur. J. Epidemiol. 9:315-321.
52. Owen, R. J., J. Bickley, A. Hurtado, A. Fraser, and R. E. Pounder. 1994. Comparison of PCR-based restriction length polymorphism analysis of ure ase genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy. J. Clin. Microbiol. 32:1203-1210.
53. Prewett, E. J., J. Bickley, R. J. Owen, and R. E. Pounder. 1992. DNA patterns of Helicobacter pylori isolated from gastric antrum, body, and duodenum. Gastroenterology 102:829-833.
54. Rautelin, H., W. Tee, K. Seppälä, and T. U. Kosunen. 1994. Ribotyping patterns and emergence of metronidazole resistance in paired clinical samples of Helicobacter pylori. J. Clin. Microbiol. 32:1079-1082.
55. Raymond, J., E. Bingen, N. Brahimi, M. Bergeret, and N. Kalach. 1996. Randomly amplified polymorphic DNA analysis in suspected laboratory Helicobacter pylori infection. Lancet i:975.
56. Romero Lopez, C., R. J. Owen, and M. Desai. 1993. Differentiation between isolates of Helicobacter pylori by PCR-RFLP analysis of urease A and B genes and comparison with ribosomal RNA gene patterns. FEMS Microbiol. Lett. 110:37-44.
57. Salama, S. M., Q. Jiang, N. Chang, R. W. Sherbaniuk, and D. E. Taylor. 1995. Characterization of chromosomal DNA profiles from Helicobacter pylori strains isolated from sequential gastric biopsy specimens. J. Clin. Microbiol. 33:2496-2497.
58. Salaün, L., C. Audibert, G. Le Lay, C. Burucoa, J. L. Fauchere, and B. Picard. 1998. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol. Lett. 161:231-239.
59. Schütze, K., E. Hentschel, B. Dragosics, and A. M. Hirschl. 1995. Helicobacter pylori reinfection with identical organisms: transmission by the patients' spouses. Gut 36:831-833.
60. Shortridge, V. D., G. G. Stone, R. K. Flamm, J. Beyer, J. Versalovic, D. W. Graham, and S. K. Tanaka. 1997. Molecular typing of Helicobacter pyloriisolates from a multicenter U.S. clinical trial by ureC restriction fragment length polymorphism. J. Clin. Microbiol. 35:471-473.
61. Stone, G. G., D. Shortridge, R. K. Flamm, J. Beyer, A. T. Ghoneim, and S. K. Tanaka. 1997. PCR-RFLP typing of ureC from Helicobacter pylori isolated from gastric biopsies during a European multi-country clinical trial. J. Antimicrob. Chemother. 40:251-256.
62. Stone, G. G., D. Shortridge, R. K. Flamm, J. Beyer, D. Stamler, and S. K. Tanaka. 1997. PCR-RFLP typing of ureC from Helicobacter pylori isolated in Argentina from gastric biopsies before and after treatment with clarithromycin. Epidemiol. Infect. 118:119-124.
63. Struelens, M. J., and the Members of the European Study Group on Epidemiological Markers (ESGEM), of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). 1996. Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. Infect. 2:2-11.
64. Takami, S., T. Hayashi, H. Akashi, Y. Tonokatsu, T. Shimoyama, and T. Tamura. 1993. Chromosomal heterogeneity of Helicobacter pylori isolates by pulse-field gel electrophoresis. Zentbl. Batteriol. Parasitenkd. Infektkrankh. Hyg. Abt. 1 Orig. 280:120-127.
65. Takami, S., T. Hayashi, H. Akashi, T. Shimoyama, and T. Tamura. 1994. Genetic heterogeneity of Helicobacter pylori by pulse-field gel electrophoresis and re-evaluation of DNA homology. Eur. J. Gastroenterol. Suppl. 6:S53-S56.
66. Taylor, D. E., M. Eaton, N. Chang, and S. M. Salama. 1992. Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level. J. Bacteriol. 174:6800-6806.
67. 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.
68. Tee, W., J. Lambert, R. Smallwood, M. Schembri, B. C. Ross, and B. Dwyer. 1992. Ribotyping of Helicobacter pylori from clinical specimens. J. Clin. Microbiol. 30:1562-1567.
69. Tyler, K. D., G. Wang, S. D. Tyler, and W. M. Johnson. 1997. Factors affecting reliability and reproducibility of amplification-based DNA finger printing of representative bacterial pathogens. J. Clin. Microbiol. 35:339-346.
70. Van der Ende, A., E. A. J. Rauws, M. Feller, C. J. J. Mulder, G. N. J. Tytgat, and J. Dankert. 1996. Heterogeneous Helicobacter pylori isolates from members of a family with a history of peptic ulcer disease. Gastroenterology 111: 638-647.
71. Van der Hulst, R. W. M., E. A. J. Rauws, B. Köycü, J. J. Keller, F. J. W. ten Kate, J. Dankert, G. N. J. Tytgat, and A. Van der Ende. 1997. Helicobacter pylori reinfection is virtually absent after successful eradication. J. Infect. Dis. 176:196-200.
72. Van Doorn, N. E., F. Namavar, J. G. Kusters, E. P. van Rees, E. J. Kuipers, and J. de Graaff. 1998. Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling. FEMS Microbiol. Lett. 160:145-150.
73. Wada, S., M. Matsuda, M. Kikuchi, T. Kodama, I. Takei, S. Ogawa, S. Takahashi, M. Shingaki, and T. Itoh. 1994. Genome DNA analysis and genotyping of clinical isolates of Helicobacter pylori. Cytobios 80:109-116.
74. Wang, J.-T., J.-C. Shell, J.-T. Lin, T.-H. Wang, and M.-S. Wu. 1993. Direct DNA amplification and restriction pattern analysis of Helicobacter pylori in patients with duodenal ulcer and their families. J. Infect. Dis. 168:1544-1548.
75. Weel, J. F. L., R. W. M. Van der Hulst, Y. Gerrits, G. N. J. Tytgat, A. Van der Ende, and J. Dankert. 1996. Heterogeneity in susceptibility to metronidazole among Helicobacter pylori isolates from patients with gastritis or peptic ulcer disease. J. Clin. Microbiol. 34:2158-2162.
76. Xia, H. X., H. J. Windle, D. G. Marshall, C. J. Smyth, C. T. Keane, and C. A. O'Morain. 1995. Recrudescence of Helicobacter pylori after apparently successful eradication: novel application of randomly amplified polymorphic DNA fingerprinting. Gut 37:30-34.