Basic Information

Faculty

• Faculty of Engineering

Professional Memberships

• American Society for Microbiology
• Japan Society on Water Environment

Academic Degree

• 修士（工学）(京都大学)
• 博士（工学）(京都大学)

ID,URL

• J-Global ID

  201601000196666536

researchmap URL

• https://researchmap.jp/7000018112

Research

Research Topics, Overview of the research

• Research Topics

  Characterization of antimicrobial-resistant Enterobacteriaceae in environmental waters

Research Interests

• One Health
• Genomic analysis
• Antimicrobial-resistant bacteria
• Enterobacteriaceae

Research Areas

• Environmental science/Agricultural science, Environmental impact assessment

Papers

• Fecal contamination and the proportion of human-associated E.coli along Nhue river, Viet Nam

  原田 英典; 五味 良太

  Vietnam Journal of Science and Technology,, 2018, Peer-reviewed

  
• Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates

  Ryota Gomi; Eiji Haramoto; Hiroyuki Wada; Yoshinori Sugie; Chih-Yu Ma; Sunayana Raya; Bikash Malla; Fumitake Nishimura; Hiroaki Tanaka; Masaru Ihara

  Science of The Total Environment, Mar. 2023

  
• Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC and SFH-1) in Enterobacterales isolated from surface waters in Japan

  Ryota Gomi; Yasufumi Matsumura; Michio Tanaka; Masaru Ihara; Yoshinori Sugie; Tomonari Matsuda; Masaki Yamamoto

  Journal of Antimicrobial Chemotherapy, 27 Apr. 2022, Peer-reviewed, Lead author, Corresponding author

  
• Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan

  Ryota Gomi; Masaki Yamamoto; Michio Tanaka; Yasufumi Matsumura

  Current Research in Microbial Sciences, Jun. 2022, Peer-reviewed, Lead author, Corresponding author

  
• Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

  Claire L. Gorrie; Mirjana Mirčeta; Ryan R. Wick; Louise M. Judd; Margaret M. C. Lam; Ryota Gomi; Iain J. Abbott; Nicholas R. Thomson; Richard A. Strugnell; Nigel F. Pratt; Jill S. Garlick; Kerrie M. Watson; Peter C. Hunter; David V. Pilcher; Steve A. McGloughlin; Denis W. Spelman; Kelly L. Wyres; Adam W. J. Jenney; Kathryn E. Holt

  Nature Communications, May 2022, Peer-reviewed

  
• Occurrence of class 1 integrons carrying two copies of the blaGES-5 gene in carbapenem-non-susceptible Citrobacter freundii and Raoultella ornithinolytica isolated from wastewater

  Ryota Gomi; Tomonari Matsuda; Masaki Yamamoto; Michio Tanaka; Thomas Jové; Pei-Hsin Chou; Yasufumi Matsumura

  Journal of Global Antimicrobial Resistance, Jul. 2021, Peer-reviewed, Lead author, Corresponding author

  
• Detection of plasmid contigs in draft genome assemblies using customized Kraken databases.

  Ryota Gomi; Kelly L Wyres; Kathryn E Holt

  Microbial Genomics, Apr. 2021, Peer-reviewed, Lead author, Corresponding author

  
• Molecular Characterization of a Multidrug-Resistance IncF Plasmid Carrying mcr-3.1 in an Escherichia coli Sequence Type 393 Strain of Wastewater Origin.

  Ryota Gomi; Tomonari Matsuda; Masaki Yamamoto; Michio Tanaka; Satoshi Ichiyama; Minoru Yoneda; Yasufumi Matsumura

  International Journal of Antimicrobial Agents, Jul. 2019, Peer-reviewed, Lead author, Corresponding author

  
• Molecular Analysis of a blaIMP-1-Harboring Class 3 Integron in Multidrug-Resistant Pseudomonas fulva.

  Masaki Yamamoto; Yasufumi Matsumura; Ryota Gomi; Tomonari Matsuda; Satoshi Nakano; Miki Nagao; Michio Tanaka; Satoshi Ichiyama

  Antimicrobial agents and chemotherapy, Aug. 2018, Peer-reviewed

  
• Pathotyping of Escherichia coli isolated from community toilet wastewater and stored drinking water in a slum in Bangladesh

  H. Harada; Y. Fujimori; R. Gomi; Md.N. Ahsan; S. Fujii; A. Sakai; T. Matsuda

  Letters in Applied Microbiology, 01 Jun. 2018, Peer-reviewed

  
• Characteristics of carbapenemase-producing enterobacteriaceae in wastewater revealed by genomic analysis

  Ryota Gomi; Tomonari Matsuda; Masaki Yamamoto; Pei-Hsin Chou; Michio Tanaka; Satoshi Ichiyama; Minoru Yoneda; Yasufumi Matsumura

  Antimicrobial Agents and Chemotherapy, 01 May 2018, Peer-reviewed, Lead author, Corresponding author

  
• Occurrence of clinically important lineages, including the ST131 C1-M27 subclone, among extended-spectrum β-lactamase-producing Escherichia coli in wastewater.

  Ryota Gomi; Tomonari Matsuda; Yasufumi Matsumura; Masaki Yamamoto; Michio Tanaka; Satoshi Ichiyama; Minoru Yoneda

  Antimicrobial Agents and Chemotherapy, Aug. 2017, Peer-reviewed, Lead author, Corresponding author

  
• Rapid identification of different Escherichia coli ST131 clades.

  Yasufumi Matsumura; Johann D D Pitout; Gisele Peirano; Rebekah DeVinney; Taro Noguchi; Masaki Yamamoto; Ryota Gomi; Tomonari Matsuda; Satoshi Nakano; Miki Nagao; Michio Tanaka; Satoshi Ichiyama

  Antimicrobial Agents and Chemotherapy, Jul. 2017, Peer-reviewed

  
• Whole-genome analysis of antimicrobialresistant and extraintestinal pathogenic Escherichia coli in river water

  Ryota Gomi; Tomonari Matsuda; Yasufumi Matsumur; Masaki Yamamoto; Michio Tanaka; Satoshi Ichiyama; Minoru Yoneda

  Applied and Environmental Microbiology, 2017, Peer-reviewed, Lead author

  
• Global Escherichia coli Sequence Type 131 Clade with bla(CTX-M-27) Gene

  Yasufumi Matsumura; Johann D. D. Pitout; Ryota Gomi; Tomonari Matsuda; Taro Noguchi; Masaki Yamamoto; Gisele Peirano; Rebekah DeVinney; Patricia A. Bradford; Mary R. Motyl; Michio Tanaka; Miki Nagao; Shunji Takakura; Satoshi Ichiyama

  Emerging Infectious Diseases, Nov. 2016, Peer-reviewed

  
• Interspecies Dissemination of a Mobilizable Plasmid Harboring bla(IMP-19) and the Possibility of Horizontal Gene Transfer in a Single Patient

  Masaki Yamamoto; Yasufumi Matsumura; Ryota Gomi; Tomonari Matsuda; Michio Tanaka; Miki Nagao; Shunji Takakura; Shinji Uemoto; Satoshi Ichiyama

  Antimicrobial Agents and Chemotherapy, Sep. 2016, Peer-reviewed

  
• Assessment of Genetic Markers for Tracking the Sources of Human Wastewater Associated Escherichia coli in Environmental Waters

  Ahmed Warish; Cheryl Triplett; Ryota Gomi; Pradip Gyawali; Leonie Hodgers; Simon Tozeti

  Environmental Science & Technology, Aug. 2015, Peer-reviewed

  
• Characterization of Pathogenic Escherichia coli in River Water by Simultaneous Detection and Sequencing of 14 Virulence Genes

  Ryota Gomi; Tomonari Matsuda; Yuji Fujimori; Hidenori Harada; Yasuto Matsui; Minoru Yoneda

  Environmental Science & Technology, Jun. 2015, Peer-reviewed, Lead author

  
• Fecal Source Tracking in Water by Next-Generation Sequencing Technologies Using Host-Specific Escherichia coli Genetic Markers

  Ryota Gomi; Tomonari Matsuda; Yasuto Matsui; Minoru Yoneda

  Environmental Science & Technology, Aug. 2014, Peer-reviewed, Lead author

  

Misc.

• The Occurrence and Source of Antimicrobial Resistant Escherichia coli in the Lake Biwa and its Basin Rivers

  杉江由規; TANG Yu; ZHAO Bo; 五味良太; 西村文武; 田中宏明; MA Chih-Yu; 井原賢

  日本水環境学会年会講演集, 2022

  
• 全ゲノム解析を取り入れた河川水中の薬剤耐性大腸菌の実態解明

  五味 良太; 松田知成; 松村康史; 山本正樹; 田中美智男; 一山智; 米田稔

  第20回日本水環境学会シンポジウム, Sep. 2017

  
• 河川水中における病原性大腸菌の実態調査

  五味良太; 松田知成; 松井康人; 米田稔

  第50回日本水環境学会年会, Mar. 2016

  
• Microbial source tracking of Escherichia coli reveals humans as a major source of fecal contamination in the Yamato River, Japan

  Gomi, R; Matsuda, T; Matsui, Y; Yoneda, M

  18th International Symposium on Health-Related Water Microbiology, Sep. 2015

  
• Microbial Source Tracking of Escherichia coli in the Yamato River Using the Basin Data and Rep-PCR DNA Fingerprinting Analysis

  五味 良太; 松井 康人; 米田 稔

  環境衛生工学研究 : 京都大学環境衛生工学研究会機関誌, Jul. 2013

  
• Novel genetic markers for identifying sources of fecal contamination in environmental water

  Gomi, R; Matsuda, T; Matsui, Y; Yoneda, M

  Environmental Health 2013, Mar. 2013

  
• Source Identification of Escherichia coli in the Yamato River using Rep-PCR DNA Fingerprinting Analysis

  五味 良太; 松井 康人; 米田 稔

  環境衛生工学研究 : 京都大学環境衛生工学研究会機関誌, Jul. 2012

  
• Relation of fecal contamination sources between river water, food and drinking water along Nhue river in Vietnam

  Mai Tanaka; Hidenori Harada; Shigeo Fujii; Min Li Chua; Ryota Gomi

  Proceedings of the Annual Conference of JSWE, 08 Mar. 2019

  
• 琵琶湖南湖から検出される大腸菌の全ゲノム解析

  井原賢; 田村太一; 五味良太; 林東範; 劉思瑶; 馬緻宇; 山下尚之; 田中宏明

  第20回日本水環境学会シンポジウム, 2017

  
• 大和川における病原性大腸菌の存在実態

  五味良太; 松田知成; 米田稔

  日本水環境学会シンポジウム講演集, 13 Sep. 2016

  

External funds: Kakenhi

• Whole-genome analysis of antimicrobial-resistant Enterobacterales in river water

  Grant-in-Aid for Early-Career Scientists

  Basic Section 63040:Environmental impact assessment-related

  Kyoto University

  Ryota Gomi

  From 01 Apr. 2019, To 31 Mar. 2022, Project Closed

  薬剤耐性菌;腸内細菌科細菌;ゲノム解析;河川;腸内細菌科

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19K20461/
• Profiling of multidrug-resistant E. coli in urban sewage in Asia and Africa by using whole-genome sequencing

  Grant-in-Aid for Challenging Research (Exploratory)

  Medium-sized Section 22:Civil engineering and related fields

  Kyoto University

  原田 英典

  From 29 Jun. 2018, To 31 Mar. 2023, Granted

  多剤耐性大腸菌;都市下水;アジア・アフリカ;全ゲノム解析

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18K18881/
• 環境水中の腸内細菌科細菌が保有する薬剤耐性プラスミドの構造解析及び伝達性評価

  Grant-in-Aid for Early-Career Scientists

  Basic Section 63040:Environmental impact assessment-related

  Kyoto University

  五味 良太

  From 01 Apr. 2022, To 31 Mar. 2025, Granted

  薬剤耐性菌;腸内細菌科細菌;ゲノム解析;プラスミド

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K18038/

Education

Teaching subject(s)

• From 01 Apr. 2023, To 31 Mar. 2024

  Data Analysis in Environmental Engineering

  3290, Fall, Faculty of Engineering, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Practice of Basic Informatics (Faculty of Engineering)

  T006, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Advanced Modern Science and Technology (4 times course)

  i055, Fall, Graduate School of Engineering, 0.5
• From 01 Apr. 2023, To 31 Mar. 2024

  Advanced Modern Science and Technology (8 times course)

  i056, Fall, Graduate School of Engineering, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Advanced Modern Science and Technology (12 times course)

  i060, Fall, Graduate School of Engineering, 1.5
• From 01 Apr. 2023, To 31 Mar. 2024

  Environmental Engineering 2, Laboratory

  3154, Fall, Faculty of Engineering, 3
• From 01 Apr. 2022, To 31 Mar. 2023

  Advanced Modern Science and Technology (12 times course)

  i060, Fall, Graduate School of Engineering, 1.5
• From 01 Apr. 2022, To 31 Mar. 2023

  Environmental Engineering 2, Laboratory

  3154, Fall, Faculty of Engineering, 3
• From 01 Apr. 2022, To 31 Mar. 2023

  Data Analysis in Environmental Engineering

  3290, Fall, Faculty of Engineering, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Practice of Basic Informatics (Faculty of Engineering)

  T006, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Advanced Modern Science and Technology (8 times course)

  i056, Fall, Graduate School of Engineering, 1
• From 01 Apr. 2022, To 31 Mar. 2023

  Advanced Modern Science and Technology (4 times course)

  i055, Fall, Graduate School of Engineering, 0.5
• From Apr. 2018, To Mar. 2019

  Fundamental Chemical Experiments

  Spring, 全学共通科目
• From Apr. 2018, To Mar. 2019

  Environmental Engineering 2, Laboratory

  Fall, 工学部
• From Apr. 2019, To Mar. 2020

  Environmental Engineering 2, Laboratory

  Fall, 工学部
• From Apr. 2020, To Mar. 2021

  Practice of Basic Informatics (Faculty of Engineering) [Global Engineering]

  Spring, 全学共通科目
• From Apr. 2020, To Mar. 2021

  Advanced Modern Science and Technology (12 times course)

  Fall, 工学研究科
• From Apr. 2020, To Mar. 2021

  Advanced Modern Science and Technology (4 times course)

  Fall, 工学研究科
• From Apr. 2020, To Mar. 2021

  Advanced Modern Science and Technology (8 times course)

  Fall, 工学研究科
• From Apr. 2020, To Mar. 2021

  Environmental Engineering , LaboratoryII

  Fall, 工学部
• From Apr. 2020, To Mar. 2021

  Data Analysis in Environmental Engineering

  Fall, 工学部
• From Apr. 2021, To Mar. 2022

  Practice of Basic Informatics (Faculty of Engineering) [Global Engineering]

  Spring, 全学共通科目
• From Apr. 2021, To Mar. 2022

  Advanced Modern Science and Technology (12 times course)

  Fall, 工学研究科
• From Apr. 2021, To Mar. 2022

  Advanced Modern Science and Technology (4 times course)

  Fall, 工学研究科
• From Apr. 2021, To Mar. 2022

  Advanced Modern Science and Technology (8 times course)

  Fall, 工学研究科
• From Apr. 2021, To Mar. 2022

  Environmental Engineering , LaboratoryII

  Fall, 工学部
• From Apr. 2021, To Mar. 2022

  Data Analysis in Environmental Engineering

  Fall, 工学部