title: Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: proposal for clone definition.
abstract: 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.
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, nr. 6, 2780-156 Oeiras, Portugal.
authors.forename: M
authors.initials: M
authors.lastname: Miragaia
authors.forename: J A
authors.initials: JA
authors.lastname: Carriço
authors.forename: J C
authors.initials: JC
authors.lastname: Thomas
authors.forename: I
authors.initials: I
authors.lastname: Couto
authors.forename: M C
authors.initials: MC
authors.lastname: Enright
authors.forename: H
authors.initials: H
authors.lastname: de Lencastre
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D002876:Chromosomes, Bacterial / Q000235:genetics; D003428:Cross Infection / Q000382:microbiology; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000382:microbiology; D013212:Staphylococcus epidermidis / Q000145:classification* / Q000235:genetics*; D013223:Statistics as Topic
chemical_list: D004269:DNA, Bacterial