Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes
João A. Carriço,Catarina Silva-Costa,José Melo-Cristino,Francisco R. Pinto,Francisco R. Pinto,H. de Lencastre,H. de Lencastre,Jonas S. Almeida,Jonas S. Almeida,Mário Ramirez +9 more
TLDR
A framework of measures for the quantitative assessment of correspondences between different typing methods is proposed as a first step to the global mapping of type equivalences and showed that if PFGE or MLST data are available one can confidently predict the emm type.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.read more
Citations
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Journal ArticleDOI
Guidelines for the validation and application of typing methods for use in bacterial epidemiology
A. van Belkum,Panayotis T. Tassios,Lenie Dijkshoorn,Sara Hæggman,Barry Cookson,Norman K. Fry,V. Fussing,Jonathan Green,Edward J. Feil,Peter Gerner-Smidt,Sylvain Brisse,Marc Struelens +11 more
TL;DR: Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages and Criteria for their evaluation and application and the interpretation of their results are proposed.
Journal ArticleDOI
Overview of molecular typing methods for outbreak detection and epidemiological surveillance
Artur J. Sabat,Ana Budimir,Nashev D,Raquel Sá-Leão,van Dijl Jm,Frédéric Laurent,Hajo Grundmann,Alexander W. Friedrich +7 more
TL;DR: Current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice are reviewed to give an overview of their specific advantages and disadvantages.
Journal ArticleDOI
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
Alexandra Moura,Alexis Criscuolo,Hannes Pouseele,Mylène M. Maury,Alexandre Leclercq,Alexandre Leclercq,Cheryl L. Tarr,Jonas T. Björkman,Timothy J. Dallman,Aleisha Reimer,Vincent Enouf,Elise Larsonneur,Heather A. Carleton,Hélène Bracq-Dieye,Hélène Bracq-Dieye,Lee S. Katz,Louis Jones,Marie Touchon,Mathieu Tourdjman,Matthew G. Walker,Steven Stroika,Thomas Cantinelli,Viviane Chenal-Francisque,Zuzana Kucerova,Eduardo P. C. Rocha,Celine Nadon,Kathie Grant,Eva Møller Nielsen,Bruno Pot,Peter Gerner-Smidt,Marc Lecuit,Sylvain Brisse +31 more
TL;DR: This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.
Journal ArticleDOI
High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli.
Scott J. Weissman,James R. Johnson,Veronika Tchesnokova,Mariya Billig,Daniel E. Dykhuizen,Kim Riddell,Peggy Rogers,Xuan Qin,Susan M. Butler-Wu,Brad T. Cookson,Ferric C. Fang,Delia Scholes,Sujay Chattopadhyay,Evgeni V. Sokurenko +13 more
TL;DR: This work describes a two-locus, sequence-based typing scheme for Escherichia coli that utilizes a 489-nucleotide (nt) internal fragment of fimH (encoding the type 1 fimbrial adhesin) and the 469-nt internal fumC fragment used in standard MLST.
Journal ArticleDOI
Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods
TL;DR: A new coefficient, the adjusted Wallace coefficient (AW), and corresponding confidence intervals (CI) are proposed as quantitative measures of congruence between typing methods and demonstrated the advantages of AW over the Wallace coefficient.
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