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Comparison of three typing methods for Pseudomonas aeruginosa isolates from patients with cystic fibrosis

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Abstract

The aim of this study was to compare two traditional pattern matching techniques, pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD), with the more reproducible technique of multilocus sequence typing (MLST) to genotype a blinded sample of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. A blinded sample of 48 well-characterized CF P. aeruginosa isolates was genotyped by PFGE, RAPD, and MLST, each performed in a different laboratory. The discriminatory power and congruence between the methods were compared using the Simpson’s index, Rand index, and Wallace coefficient. PFGE and MLST had the greatest congruence with the highest Rand index (0.697). The discriminatory power of PFGE, RAPD, and MLST were comparable, with high Simpson’s indices (range 0.973–0.980). MLST identified the most clonal relationships. When clonality was defined as agreement between two or more methods, MLST had the greatest predictive value (100 %) in labeling strains as unique, while PFGE had the greatest predictive value (96 %) in labeling strains as clonal. This study demonstrated the highest level of agreement between PFGE and MLST in genotyping P. aeruginosa isolates from CF patients. MLST had the greatest predictive value in identifying strains as unique and, thus, has the potential to be a cost-efficient, high-throughput, first-pass typing method.

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Acknowledgments

We gratefully acknowledge the assistance of Ms. Danuta Kovach, Mr. Trevor Hird, Mr. Bradley Locke, Ms. Lisa Louie, Mr. Craig Diegel, Dr. Sylva Donaldson, and Dr. Pauline Wang. This work was funded, in part, by Canada Research Chair support to D.S.G., and Cystic Fibrosis Canada (operating grant to V.W., D.P.S., and salary award to J.E.A.Z.).

Conflicts of interest

All of the authors have no conflict of interest to declare.

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Authors and Affiliations

  1. Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada

    V. Waters

  2. Division of Infectious and Immunological Diseases, Department of Pediatrics, Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia, V5Z 4H4, Canada

    J. E. A. Zlosnik & D. P. Speert

  3. Division of Microbiology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada

    Y. C. W. Yau

  4. Division of Respiratory Medicine, Department of Medicine, Ottawa Hospital Research Institute, University of Ottawa, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada

    S. D. Aaron

  5. Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada

    D. S. Guttman

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  1. V. Waters
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Correspondence to V. Waters.

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Waters, V., Zlosnik, J.E.A., Yau, Y.C.W. et al. Comparison of three typing methods for Pseudomonas aeruginosa isolates from patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 31, 3341–3350 (2012). https://doi.org/10.1007/s10096-012-1701-z

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  • DOI: https://doi.org/10.1007/s10096-012-1701-z

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