GAS-J

GAS-J performs emm typing, MLST typing, virulence factor gene detection, and phylogenetic tree analysis of Streptococcus pyogenes from whole genome sequencing data.

Key Features:

• emm typing: Identifies emm types from whole genome data, including detection of pseudo-emm (emm-like) genes, with results matching conventional PCR and Sanger sequencing.
• MLST typing: Determines sequence types (STs) by performing BLAST searches using seven alleles as references.
• Virulence factor gene detection: Detects carriage of virulence factor genes using a curated dataset containing 620 related proteins.
• Phylogenetic tree construction: Generates SNP-based phylogenetic trees with user-selected isolates from a pool of 406 isolates with epidemiological data, including isolates diagnosed with STSS or non-STSS based on the STSS criteria of the Japan Communicable Disease Prevention Law.
• Genome assembly: Accepts raw short-read data and includes the velvet assembler for de novo genome assembly.

Scientific Applications:

• Streptococcus pyogenes strain characterization: Classifies clinical isolates using emm typing and MLST analysis from whole genome sequencing data.
• Virulence profiling: Identifies presence of virulence factor genes to assess pathogenic potential of isolates.
• Epidemiological surveillance: Enables comparison of isolates with epidemiological data for outbreak investigation and population structure analysis.
• STSS research: Supports analysis of isolates associated with streptococcal toxic shock syndrome versus non-STSS cases.

Methodology:

GAS-J accepts raw short-read data as input and uses the velvet assembler for genome assembly. emm types are determined from assembled genomes. STs are determined by performing BLAST search using seven alleles as references. Virulence factor genes are detected using a dataset of 620 related proteins. SNP-based phylogenetic trees are constructed from user-selected isolates.