title: Streptococcus pyogenes strains in Sao Paulo, Brazil: molecular characterization as a basis for StreptInCor coverage capacity analysis.
abstract: BACKGROUND
  Several human diseases are caused by Streptococcus pyogenes, ranging from common infections to autoimmunity. Characterization of the most prevalent strains worldwide is a useful tool for evaluating the coverage capacity of vaccines under development. In this study, a collection of S. pyogenes strains from Sao Paulo, Brazil, was analyzed to describe the diversity of strains and assess the vaccine coverage capacity of StreptInCor.
  
  
  METHODS
  Molecular epidemiology of S. pyogenes strains was performed by emm-genotyping the 229 isolates from different clinical sites, and PCR was used for superantigen profile analysis. The emm-pattern and tissue tropism for these M types were also predicted and compared based on the emm-cluster classification.
  
  
  RESULTS
  The strains were fit into 12 different emm-clusters, revealing a diverse phylogenetic origin and, consequently, different mechanisms of infection and escape of the host immune system. Forty-eight emm-types were distinguished in 229 samples, and the 10 most frequently observed types accounted for 69 % of all isolates, indicating a diverse profile of circulating strains comparable to other countries under development. A similar proportion of E and A-C emm-patterns were observed, whereas pattern D was less frequent, indicating that the strains of this collection primarily had a tissue tropism for the throat. In silico analysis of the coverage capacity of StreptInCor, an M protein-conserved regionally based vaccine candidate developed by our group, had a range of 94.5 % to 59.7 %, with a mean of 71.0 % identity between the vaccine antigen and the predicted amino acid sequence of the emm-types included here.
  
  
  CONCLUSIONS
  This is the first report of S. pyogenes strain characterization in Sao Paulo, one of the largest cities in the world; thus, the strain panel described here is a representative sample for vaccine coverage capacity analysis. Our results enabled evaluation of StreptInCor candidate vaccine coverage capacity against diverse M-types, indicating that the vaccine candidate likely would induce protection against the diverse strains worldwide.
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. sfreschi@usp.br.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. sfreschi@usp.br.
authors.forename: Samar
authors.initials: S
authors.lastname: Freschi de Barros
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. karineamicis@gmail.com.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. karineamicis@gmail.com.
authors.forename: Karine Marafigo
authors.initials: KM
authors.lastname: De Amicis
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. quelalencar@yahoo.com.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. quelalencar@yahoo.com.
authors.forename: Raquel
authors.initials: R
authors.lastname: Alencar
authors.affiliation: Laboratoire de Génétique et Physiologie Bactérienne, Institute de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, Bruxelles, 1050, Belgium. pierre.smeesters@mcri.edu.au.|Murdoch Childrens Research Institute, Parkville, 3052, Australia. pierre.smeesters@mcri.edu.au.
authors.forename: Pierre Robert
authors.initials: PR
authors.lastname: Smeesters
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. attsp@uol.com.br.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. attsp@uol.com.br.
authors.forename: Ariel
authors.initials: A
authors.lastname: Trunkel
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. edilpostol@yahoo.com.br.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. edilpostol@yahoo.com.br.
authors.forename: Edilberto
authors.initials: E
authors.lastname: Postól
authors.affiliation: Microbiology Laboratory of Clinical Hospital, School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. jnaj99@gmail.com.
authors.forename: João Nóbrega
authors.initials: JN
authors.lastname: Almeida Junior
authors.affiliation: Microbiology Laboratory of Clinical Hospital, School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. flaviarossi61@gmail.com.
authors.forename: Flavia
authors.initials: F
authors.lastname: Rossi
authors.affiliation: Special Clinical Microbiolgy Laboratory (LEMC), Federal Univeristy of São Paulo/UNIFESP, São Paulo, Brazil. pignatari@terra.com.br.
authors.forename: Antonio Carlos Campos
authors.initials: AC
authors.lastname: Pignatari
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. jkalil@usp.br.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. jkalil@usp.br.|Clinical Immunology and Allergy Division, School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. jkalil@usp.br.
authors.forename: Jorge
authors.initials: J
authors.lastname: Kalil
authors.affiliation: Heart Institute (InCor), School of Medicine, University of Sao Paulo, Sao Paulo, 01246-000, Brazil. luizagui@usp.br.|Institute for Immunology Investigation, National Institute of Science and Technology, Sao Paulo, 01246-000, Brazil. luizagui@usp.br.|Laboratory of Immunology, Clinical Hospital, Heart Institute (HC-FMUSP), Av. Dr. Enéas de Carvalho Aguiar, 44, Sao Paulo, 05403-000, Brazil. luizagui@usp.br.
authors.forename: Luiza
authors.initials: L
authors.lastname: Guilherme
mesh_terms: D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000032:analysis / Q000235:genetics; D001428:Bacterial Vaccines / Q000276:immunology*; D001938:Brazil / Q000453:epidemiology; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification / Q000378:metabolism; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D013290:Streptococcal Infections / Q000453:epidemiology / Q000473:pathology / Q000517:prevention & control*; D013297:Streptococcus pyogenes / Q000145:classification / Q000235:genetics / Q000276:immunology*; D018089:Superantigens / Q000032:analysis / Q000235:genetics
chemical_list: D000942:Antigens, Bacterial; D001428:Bacterial Vaccines; D004269:DNA, Bacterial; D018089:Superantigens