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Detection of superantigens in Streptococcus pyogenes isolates based on whole genome sequencing data

R Veselá, S Vohrnová, J Kozáková

    Epidemiologie, Mikrobiologie, Imunologie : Casopis Spolecnosti Pro Epidemiologii a Mikrobiologii Ceske Lekarske Spolecnosti J.E. Purkyne
    |October 23, 2023
    PubMed

    Insights

    Bioinformatics tools now aid in analyzing Streptococcus pyogenes whole genome sequencing (WGS) data. This helps identify key virulence factors like M protein and superantigens in invasive strains.

    Area of Science:

    • Microbiology
    • Genomics
    • Bioinformatics

    Background:

    • Streptococcus pyogenes causes diverse human diseases, from skin infections to invasive conditions like toxic shock syndrome.
    • Virulence factors include M protein (emm gene) and pyrogenic exotoxins (superantigens).
    • Advancements in whole genome sequencing (WGS) offer new analytical possibilities.

    Purpose of the Study:

    • To evaluate newly implemented bioinformatics tools for processing S. pyogenes WGS data.
    • To characterize emm type, sequence type, and superantigen gene profiles of invasive S. pyogenes isolates.

    Main Methods:

    • Whole genome sequencing (WGS) data from 10 invasive S. pyogenes isolates were analyzed.
    • SRST2 software and the BV-BRC platform were utilized for data processing.
    • Unicycler assembly pipeline with SPAdes de novo assembler was employed for genome assembly from short reads.

    Main Results:

    • Bioinformatics tools successfully determined emm type, sequence type, and superantigen profiles.
    • Genome assembly from short reads was achieved using the Unicycler/SPAdes pipeline.
    • Characterization of virulence factor genes in invasive strains was performed.

    Conclusions:

    • Newly introduced bioinformatics tools are effective for analyzing S. pyogenes WGS data.
    • These tools facilitate the identification of critical virulence factors in invasive strains.
    • This approach enhances the understanding of S. pyogenes pathogenesis and epidemiology.
    Keywords:
    GASStreptococcus pyogenessuperantigenwhole genome sequencing

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