Detection of superantigens in Streptococcus pyogenes isolates based on whole genome sequencing data.
R VeseláS VohrnováJ KozákováPublished in: Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne (2023)
Streptococcus pyogenes causes a variety of human diseases ranging from uncomplicated respiratory tract and skin infections to severe invasive diseases possibly involving toxic shock syndrome. Besides the emm gene-encoded M protein, important virulence factors are pyrogenic exotoxins, referred to as superantigens. The National Reference Laboratory for Streptococcal Infections has newly introduced bioinformatics tools for processing S. pyogenes whole genome sequencing data. Using the SRST2 software and BV-BRC platform, WGS data of 10 S. pyogenes isolates from patients with invasive disease were analysed, and emm type, sequence type, and superantigen encoding gene profiles were determined. The Unicycler assembly pipeline with the SPAdes de novo assembler was used to assemble genome sequences from short reads.
Keyphrases
- respiratory tract
- electronic health record
- genome wide
- big data
- escherichia coli
- endothelial cells
- pseudomonas aeruginosa
- candida albicans
- data analysis
- staphylococcus aureus
- quality improvement
- amino acid
- machine learning
- dna methylation
- binding protein
- protein protein
- small molecule
- early onset
- inflammatory response
- genetic diversity
- soft tissue
- transcription factor
- genome wide identification
- loop mediated isothermal amplification
- genome wide analysis