title: Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.
abstract: The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant Streptococcus pyogenes isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping, emm sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the emm type (Wallace coefficients of 0.952 for both methods). In contrast, emm typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes.
authors.affiliation: Grupo de Biomatemática, Istituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6 2780-156 Oeiras, Portugal. jcarrico@itqb.unl.pt
authors.forename: J A
authors.initials: JA
authors.lastname: Carriço
authors.forename: C
authors.initials: C
authors.lastname: Silva-Costa
authors.forename: J
authors.initials: J
authors.lastname: Melo-Cristino
authors.forename: F R
authors.initials: FR
authors.lastname: Pinto
authors.forename: H
authors.initials: H
authors.lastname: de Lencastre
authors.forename: J S
authors.initials: JS
authors.lastname: Almeida
authors.forename: M
authors.initials: M
authors.lastname: Ramirez
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D000942:Antigens, Bacterial; D001425:Bacterial Outer Membrane Proteins; D015373:Bacterial Typing Techniques / Q000706:statistics & numerical data*; D002352:Carrier Proteins; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D015252:Deoxyribonucleases, Type II Site-Specific; D024881:Drug Resistance, Bacterial; D016521:Electrophoresis, Gel, Pulsed-Field; D006801:Humans; D018942:Macrolides / Q000494:pharmacology; D008826:Microbial Sensitivity Tests; D010612:Pharyngitis / Q000382:microbiology; D011174:Portugal; D017422:Sequence Analysis, DNA; D012703:Serotyping; D013290:Streptococcal Infections / Q000382:microbiology; D013297:Streptococcus pyogenes / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000276:immunology
chemical_list: D000900:Anti-Bacterial Agents; D000942:Antigens, Bacterial; D001425:Bacterial Outer Membrane Proteins; D002352:Carrier Proteins; D004269:DNA, Bacterial; D018942:Macrolides; C014689:streptococcal M protein; C041749:endodeoxyribonuclease SfiI; C025651:CCCGGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific