Fig. 1
Genomic characterization of group A Streptococcus pyogenes clinical strains isolated from oropharynx swabs. Streptococcus pyogenes isolates obtained following admission in first aid care unit for respiratory symptoms from oropharynx specimen were genotypically characterized by whole genome sequencing. The experimental design, including the isolate cultured and sequenced number, is schematically represented in Supplementary Figure 1. Each genomic DNA was achieved from pure culture, processed to obtain an Illumina tagmented-based library and finally sequenced using an Illumina MiSeq instrument. Short reads raw data were quality checked to exclude contamination, de novo aligned and the final obtained contigs used as template to search for virulence genes and antimicrobial determinants. Sequencing details are reported in Supplementary data 1, whereas the bioinformatic tools used for the analysis are summarized in the Supplementary data 8. a. Minimum spanning tree shows phylogenetic distances among GAS isolates. Colours are associated to sequence type identification. Each number indicates the distances between two or more isolates, while a node with more isolates or the marked connection between more isolated highlights clonal strains (less than six single nucleotide variants). b. A maximum likelihood phylogenetic tree of the GAS isolates was generated with the cgMLST by using RidomSeqSphere. The heatmap summarizing sequence type (ST, tip points), emm-type, emm-cluster, virulence (blue: gene presence) and antimicrobial resistance (red: gene presence) genes and prophages and ICEs/IMEs was provided by using ggtree package. Virulence genes associated with prophage regions were evidenced with the symbol asterisk.
