This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Johnson, J. R.
Right arrow Articles by O'Bryan, T. T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Johnson, J. R.
Right arrow Articles by O'Bryan, T. T.

 Previous Article  |  Next Article 

Clinical and Diagnostic Laboratory Immunology, March 2000, p. 265-273, Vol. 7, No. 2
1071-412X/00/$04.00+0

Improved Repetitive-Element PCR Fingerprinting for Resolving Pathogenic and Nonpathogenic Phylogenetic Groups within Escherichia coli

James R. Johnson* and Timothy T. O'Bryan

VA Medical Center and Department of Medicine, University of Minnesota, Minneapolis, Minnesota

Received 6 August 1999/Returned for modification 3 November 1999/Accepted 7 December 1999

Repetitive-element PCR (rep-PCR) fingerprinting is a promising molecular typing tool for Escherichia coli, including for discriminating between pathogenic and nonpathogenic clones, but is plagued by irreproducibility. Using the ERIC2 and BOXA1R primers and 15 E. coli strains from the ECOR reference collection (three from each phylogenetic group, as defined by multilocus enzyme electrophoresis [MLEE], including virulence-associated group B2), we rigorously assessed the effect of extremely elevated annealing temperatures on rep-PCR's reproducibility, discriminating power, and ability to reveal MLEE-defined phylogenetic relationships. Modified cycling conditions significantly improved assay reproducibility and discriminating power, allowing fingerprints from different cyclers to be analyzed together with minimal loss of resolution. The correspondence of rep-PCR with MLEE with respect to tree structure and regression analysis of distances was substantially better with modified than with standard cycling conditions. Nonetheless, rep-PCR was only a fair surrogate for MLEE, and when fingerprints from different days were compared, it failed to distinguish between different clones within all-important phylogenetic group B2. These findings indicate that although the performance and phylogenetic fidelity of rep-PCR fingerprinting can be improved substantially with modified assay conditions, even when so improved rep-PCR cannot fully substitute for MLEE as a phylogenetic typing method for pathogenic E. coli.

* Corresponding author. Mailing address: Infectious Diseases (111F), VA Medical Center, One Veterans Dr., Minneapolis, MN 55417. Phone: (612) 725-2000, ext. 4185, Fax: (612) 725-2273. E-mail: johns007{at}tc.umn.edu.

Clinical and Diagnostic Laboratory Immunology, March 2000, p. 265-273, Vol. 7, No. 2
1071-412X/00/$04.00+0


This article has been cited by other articles:

  • Tartof, S. Y., Solberg, O. D., Manges, A. R., Riley, L. W. (2005). Analysis of a Uropathogenic Escherichia coli Clonal Group by Multilocus Sequence Typing. J. Clin. Microbiol. 43: 5860-5864 [Abstract] [Full Text]  
  • Singer, R. S., Patterson, S. K., Meier, A. E., Gibson, J. K., Lee, H. L., Maddox, C. W. (2004). Relationship between Phenotypic and Genotypic Florfenicol Resistance in Escherichia coli. Antimicrob. Agents Chemother. 48: 4047-4049 [Abstract] [Full Text]  
  • Johnson, J. R., Owens, K., Sabate, M., Prats, G. (2004). Rapid and Specific Detection of the O15:K52:H1 Clonal Group of Escherichia coli by Gene-Specific PCR. J. Clin. Microbiol. 42: 3841-3843 [Abstract] [Full Text]  
  • Johnson, J. R., Owens, K., Manges, A. R., Riley, L. W. (2004). Rapid and Specific Detection of Escherichia coli Clonal Group A by Gene-Specific PCR. J. Clin. Microbiol. 42: 2618-2622 [Abstract] [Full Text]  
  • Meacham, K. J., Zhang, L., Foxman, B., Bauer, R. J., Marrs, C. F. (2003). Evaluation of Genotyping Large Numbers of Escherichia coli Isolates by Enterobacterial Repetitive Intergenic Consensus-PCR. J. Clin. Microbiol. 41: 5224-5226 [Abstract] [Full Text]  
  • McLellan, S. L., Daniels, A. D., Salmore, A. K. (2003). Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting. Appl. Environ. Microbiol. 69: 2587-2594 [Abstract] [Full Text]  
  • Cao, V., Lambert, T., Nhu, D. Q., Loan, H. K., Hoang, N. K., Arlet, G., Courvalin, P. (2002). Distribution of Extended-Spectrum {beta}-Lactamases in Clinical Isolates of Enterobacteriaceae in Vietnam. Antimicrob. Agents Chemother. 46: 3739-3743 [Abstract] [Full Text]  
  • Johnson, J. R., Stell, A. L., O'Bryan, T. T., Kuskowski, M., Nowicki, B., Johnson, C., Maslow, J. N., Kaul, A., Kavle, J., Prats, G. (2002). Global Molecular Epidemiology of the O15:K52:H1 Extraintestinal Pathogenic Escherichia coli Clonal Group: Evidence of Distribution beyond Europe. J. Clin. Microbiol. 40: 1913-1923 [Abstract] [Full Text]  
  • Kumao, T., Ba-Thein, W., Hayashi, H. (2002). Molecular Subtyping Methods for Detection of Salmonella enterica Serovar Oranienburg Outbreaks. J. Clin. Microbiol. 40: 2057-2061 [Abstract] [Full Text]  
  • Clermont, O., Cordevant, C., Bonacorsi, S., Marecat, A., Lange, M., Bingen, E. (2001). Automated Ribotyping Provides Rapid Phylogenetic Subgroup Affiliation of Clinical Extraintestinal Pathogenic Escherichia coli Strains. J. Clin. Microbiol. 39: 4549-4553 [Abstract] [Full Text]  
  • Manges, A. R., Johnson, J. R., Foxman, B., O'Bryan, T. T., Fullerton, K. E., Riley, L. W. (2001). Widespread Distribution of Urinary Tract Infections Caused by a Multidrug-Resistant Escherichia coli Clonal Group. NEJM 345: 1007-1013 [Abstract] [Full Text]  
  • Johnson, J. R., Clabots, C., Azar, M., Boxrud, D. J., Besser, J. M., Thurn, J. R. (2001). Molecular Analysis of a Hospital Cafeteria-Associated Salmonellosis Outbreak Using Modified Repetitive Element PCR Fingerprinting. J. Clin. Microbiol. 39: 3452-3460 [Abstract] [Full Text]  
  • Johnson, J. R., Stell, A. L., Kaster, N., Fasching, C., O'Bryan, T. T. (2001). Novel Molecular Variants of Allele I of the Escherichia coli P Fimbrial Adhesin Gene papG. Infect. Immun. 69: 2318-2327 [Abstract] [Full Text]  
  • Johnson, J. R., Stell, A. L., Delavari, P. (2001). Canine Feces as a Reservoir of Extraintestinal Pathogenic Escherichia coli. Infect. Immun. 69: 1306-1314 [Abstract] [Full Text]  
  • Johnson, J. R., Clabots, C. (2000). Improved Repetitive-Element PCR Fingerprinting of Salmonella enterica with the Use of Extremely Elevated Annealing Temperatures. CVI 7: 258-264 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»