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. 2025 Jul;69(7):384-388.
doi: 10.1111/1348-0421.13223. Epub 2025 Apr 20.

GAS-J, a User-Friendly Browser Application for Genome Assembly, emm-Typing, MLST Typing, and Virulence Factor Gene Detection of Streptococcus pyogenes

Norihiko Takemoto  1 , Kohei Ogura  2 , Yuan Gao  3 , Rumi Okuno  4 , Masaya Yamaguchi  5   6   7   8   9 , Yujiro Hirose  8 , Masayuki Ono  6   8 , Shigetada Kawabata  8   9 , Tadayoshi Ikebe  10 , Takashi Hamabata  1 , Tohru Miyoshi-Akiyama  1
Affiliations

GAS-J, a User-Friendly Browser Application for Genome Assembly, emm-Typing, MLST Typing, and Virulence Factor Gene Detection of Streptococcus pyogenes

Norihiko Takemoto et al. Microbiol Immunol. 2025 Jul.

Abstract

Clinical isolates of Streptococcus pyogenes are usually classified using emm and multilocus sequence typing (MLST). Recently, whole genome sequencing (WGS) has been employed for emm typing and MLST analysis. WGS data provides additional information on the presence of virulence factor genes. To enable researchers unfamiliar with bioinformatics to analyze WGS data of S. pyogenes, we opened an online tool named GAS-J, which automatically outputs emm types, sequence types (STs), carriage of virulence factor genes, and phylogenetic trees. The tool accepts raw short-read data as inputs, since it includes the velvet assembler. In all isolates, the emm typing results from this tool were identical to those obtained by conventional PCR and Sanger sequencing, even in cases where isolates had pseudo-emm (emm-like) genes. STs are determined by performing a BLAST search using seven alleles as references. To detect S. pyogenes virulence factor genes, we prepared a new data set containing 620 related proteins. Users may choose which isolates to include in SNP-based phylogenetic tree from a pool of 406 isolates with epidemiological data. The data set includes isolates whose symptoms (STSS or non-STSS) were diagnosed based on the STSS criteria of the Japan Communicable Disease Prevention Law. GAS-J application is available at http://gasj.ncgm.go.jp. The data of isolates are going to be updated in the future.

Keywords: Streptococcus pyogenes; emm typing; multilocus sequence typing; virulence factor; web tool.

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Conflict of interest statement

The authors declare no conflicts of interest. Kohei Ogura is an Editorial Board member and is also a coauthor of this article. To minimize bias, he was excluded from all editorial decision‐making related to the acceptance of this article for publication. Late Tohru Miyoshi‐Akiyama served on the Editorial Board until 2023, but is no longer a member of the Board and is therefore not involved in any editorial decision‐making.

Figures

Figure 1
Figure 1
Overview of the online tool. The tool accepts assembled sequences and raw short‐read data of Streptococcus pyogenes as inputs, and detects emm types, sequence types (STs), carriage of virulence factor genes, and phylogenetic trees.
Figure 2
Figure 2
Example screenshots of the analysis. Users can upload assembled genome sequences and raw short‐read data, selecting options such as emm typing, MLST, phylogenetic analysis parameters, and virulence factor detection.
See this image and copyright information in PMC

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