Need for Whole-genome Sequencing of Antimicrobial-resistant Organisms in Nosocomial Outbreak Investigations and the Concept of Prospective Analyses

Kotaro Aoki

doi:10.4058/jsei.40.259

November 25, 2025Japanese Journal of Infection Prevention and ControlOpen Access

Need for Whole-genome Sequencing of Antimicrobial-resistant Organisms in Nosocomial Outbreak Investigations and the Concept of Prospective Analyses

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Key Points

The research emphasizes the necessity of whole-genome sequencing for analyzing antimicrobial-resistant organisms in hospital outbreaks.
Whole-genome sequencing of bacterial samples during nosocomial outbreak investigations.
Analysis of cgSNP (core-genome single nucleotide polymorphism) to identify genetic relationships.
Development of a workflow for timely feedback to infection control teams.
Identified critical antimicrobial resistance genes using whole-genome sequencing.
Demonstrated the effectiveness of cgSNP analysis in understanding outbreak dynamics.
Proposed a structured process for integrating genomic data into infection control practices.

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Implication

Investigates whole-genome sequencing for timely antimicrobial resistance tracking in hospitals, suggesting enhanced infection control measures.

Abstract

細菌の全ゲノム解析はあらゆる解析を1度に実行できる強力な方法である．具体例には，菌種同定，薬剤耐性遺伝子や病原遺伝子の網羅的検索，遺伝子アリルタイピング，プラスミド解析だけでなく，コアゲノム中の一塩基置換（cgSNP）に基づく系統/遺伝的距離解析が可能である．本稿では，細菌の院内アウトブレイク調査における全ゲノム解析を用いたcgSNP解析の必要性を述べ，その今後の活用のために筆者の研究グループが提案する“Tracking Antimicrobial Resistant Organisms Timely：TAROT”という逐次cgSNP解析の結果をタイムリーに院内感染対策チームへフィードバックするというコンセプトとそれを微生物検査室内で実現するために開発したワークフローを紹介する．

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Kotaro Aoki (2025) studied this question.

synapsesocial.com/papers/6a1689510c924ddd1bd5814d https://doi.org/10.4058/jsei.40.259

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Need for Whole-genome Sequencing of Antimicrobial-resistant Organisms in Nosocomial Outbreak Investigations and the Concept of Prospective Analyses

Key Points

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Abstract

Discussion

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Need for Whole-genome Sequencing of Antimicrobial-resistant Organisms in Nosocomial Outbreak Investigations and the Concept of Prospective Analyses

Key Points

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Implication

Abstract

Discussion

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