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Journal of Clinical Microbiology, January 2008, p. 118-129, Vol. 46, No. 1
0095-1137/08/$08.00+0     doi:10.1128/JCM.01685-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Comparison of Molecular Typing Methods for Characterization of Staphylococcus epidermidis: Proposal for Clone Definition ^,

Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, nr. 6, 2780-156 Oeiras, Portugal,¹ Knowledge Discovery in Bioinformatics Group, Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento, Rua Alves Redol nr. 9, Apartado 13069, 1000-029 Lisboa, Portugal,² Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, Old Medical School Building, St Mary's Hospital, Norfolk Place, London W2 1PG, United Kingdom,³ UEI Micobactérias, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, nr. 96, 1349-008 Lisboa, Portugal,⁴ Centro de Recursos Microbiológicos, Faculdade de Ciências e Tecnologia, Quinta da Torre, 2829-516 Monte de Caparica, Portugal,⁵ Laboratory of Microbiology, The Rockefeller University, New York, New York 10021⁶

Received 23 August 2007/ Returned for modification 13 October 2007/ Accepted 25 October 2007

In the present study we give some direction on the selection of the most appropriate typing method(s) to be used for the characterization of Staphylococcus epidermidis, in view of the most recent findings on the evolution, population structure, and epidemiology of this species. In order to achieve this aim, quantitative assessment of the correlation of the results of three typing methods—pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal chromosomal cassette mec (SCCmec) typing, which target different regions of the chromosome that evolve at different rates—was performed. In order to evaluate the discriminatory ability and the strength and direction of the correlation of the different typing methods, Simpson's index of diversity (SID), the adjusted Rand coefficient (AR), and the Wallace coefficient (W) were calculated. PFGE was the most discriminatory method (SID = 99%), followed by MLST (SID = 90%) and SCCmec typing (SID = 75%). The values of AR and W (0.10 < AR < 0.30; 0.50 < W < 0.75) indicated that the partition of the same isolate collection by PFGE, MLST, and SCCmec typing provided results that had only a poor correlation with each other. However, the information provided by the combination of PFGE and SCCmec enabled the prediction of the results obtained by MLST at the level of the clonal complex with a high degree of precision (W > 0.90). We propose that clones of S. epidermidis be defined by the combination of the PFGE type followed by the SCCmec type, which provides reliable information on the short-term epidemiology and the ability to predict with consistency long-term clonal evolution.

Published ahead of print on 7 November 2007.

Supplemental material for this article may be found at http://jcm.asm.org/.