Development of the GARAPON method for estimating the prevalence of antimicrobial resistance gene in each bacterial species in water environment

2023 Fiscal Year Final Research Report

• Project/Area Number: 22K19848
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 63:Environmental analyses and evaluation and related fields
• Research Institution: Ehime University
• Principal Investigator: Watanabe Kozo 愛媛大学, 沿岸環境科学研究センター, 教授 (80634435)
• Co-Investigator(Kenkyū-buntansha): 鈴木 聡 愛媛大学, 理工学研究科(工学系), 寄附講座教授 (90196816)
• Project Period (FY): 2022-06-30 – 2024-03-31
• Keywords: 薬剤耐性菌 / メタバーコーディング解析

Outline of Final Research Achievements

To estimate "which species" of bacterial communities in water environments possess "which antibiotic resistance genes," we developed a method called Gene Analysis of Randomized Populations (GARAPON), which estimates the species possessing resistance genes based on changes in the resistance gene possession rate of sample bacterial communities whose community structure (species composition and relative abundance of each species) was forcibly altered from the original bacterial community. The accuracy of the estimates varied significantly depending on the resistance gene. Among the eight resistance genes targeted for estimation, the resistance genes aada2, tetM, and tetG, possessed by only 9, 7, and 3 genera out of 37, respectively, were estimated with relatively high accuracy rates of 3/9, 4/7, and 3/3.

Free Research Field

環境工学

Academic Significance and Societal Importance of the Research Achievements

本研究で開発したガラポン法の精度を更に向上させることで，薬剤耐性菌研究にブレークスルーを起こすこととなる。例えば，薬剤耐性遺伝子の病原菌への種間の水平伝播が，環境中の主要な培養不可菌を起源（リザバー）とする現象が証明できれば，細菌群集全体を俯瞰した薬剤耐性遺伝子の環境中動態の解明を可能にする。さらに，薬剤耐性菌だけではなく，例えば，環境微生物から有用な機能性遺伝子（例，環境浄化遺伝子）を有する種を探索する研究分野においても，培養不可菌を含む幅広い細菌からの種の探索を可能にするなど，その適用範囲は極めて広い。