Evidence map›Paper›PMID 40253701›Full record

ArticleMicrobiology and immunology2025

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

Norihiko Takemoto, Kohei Ogura, Yuan Gao, Rumi Okuno, Masaya Yamaguchi, Yujiro Hirose, Masayuki Ono, Shigetada Kawabata, Tadayoshi Ikebe, Takashi Hamabata and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbiology and immunology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Complete genome sequences of 20Microbiology resource announcements · 2026
    Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Norihiko TakemotoDepartment of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Kohei OguraLaboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Yuan GaoTokyo College of Medico-Pharmaco-Nursing Technology, Tokyo, Japan.
Rumi OkunoDepartment of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Masaya YamaguchiLaboratory of Microbial Informatics, Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
Yujiro HiroseDepartment of Microbiology, Graduate, School of Dentistry, Osaka University, Osaka, Japan.
Masayuki OnoBioinformatics Research Unit, Graduate School of Dentistry, Osaka University, Osaka, Japan.
Shigetada KawabataDepartment of Microbiology, Graduate, School of Dentistry, Osaka University, Osaka, Japan.
Tadayoshi IkebeDepartment of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.ORCID http://orcid.org/0000-0003-1021-1728
Takashi HamabataDepartment of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Tohru Miyoshi-AkiyamaDepartment of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.

Funding

This study was supported by the National Center for Global Health and Medicine and the Japan Agency for Medical Research and Development.
6 · The paper itself

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.

Indexed as

Antigens, BacterialBacterial Outer Membrane ProteinsCarrier ProteinsGenome, BacterialMultilocus Sequence TypingSoftwareStreptococcus pyogenesVirulence FactorsComputational BiologyHumansPhylogenyPolymorphism, Single NucleotideStreptococcal InfectionsWhole Genome SequencingAntigens, BacterialBacterial Outer Membrane ProteinsCarrier Proteinsstreptococcal M proteinVirulence Factorsemm typingmultilocus sequence typingStreptococcus pyogenesvirulence factorweb tool

Identifiers

PMID40253701
PMCPMC12232109

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.