Prof Fiona Walsh

    Biology, Human Health Institute

    Professor

    Biosciences & Electronic Engineering Facility
    B1.24
    (01) 474 7246

    Biography

    BSc (HONS) 1st Microbiology NUI Galway 1998 PhD Medical Microbiology University of Edinburgh 2003 Post-Doctoral Researcher University of Edinburgh 2003 - 2005 Health Research Board Fellow & Post-Doctoral Researcher Trinity College Dublin 2005 - 2009 Senior Post-Doctoral Researcher Swiss Federal Department of Agriculture Research Station 2009 - 2013

    Research Interests

    I am one of only a few people worldwide that has investigated antimicrobial resistance (AMR) across the three areas of One Health: human, animal, and environment. I have created the collaborative networks and experiments to enable me and subsequently others within

    bacteriology to investigate AMR from many angles. Plasmid mediated AMR has been a constant thread running through my research from PhD to current projects as understanding the mobile AMR mechanisms across biomes is a major area of my research. The papers that I have published reflect this spectrum of research adaptability and interests. I took a risk during my career and moved from investigating AMR in human pathogens to investigating AMR in soil, plant, animal, and environmental biomes. This unusual career path has enabled me to identify the gaps in our knowledge and research understanding of the constant flow of AMR genes across biomes. My research has influenced EU policy under the water framework directive in the inclusion of specific antimicrobials in the watch list and my position as a unique researcher and leader in the niche area of AMR mobility across biomes has been recognised by invitations to speak at international leading conferences and membership of policy influencing committees. I am the founder and director of the Antimicrobial Resistance Research Centre, based at Maynooth University. I formulated the concept of a trans-disciplinary network of researchers across Ireland spanning microbiology, chemistry, immunology, economics, psychology, and law to develop collaborations in AMR.

    Research Projects

    Title Role Description Start date End date Amount
    Research Gap Analysis Antimicrobial Resistance and the Environment PI 02/10/2020 02/06/2021 3380
    Animal artificial microbiome platform PI 01/09/2020 31/12/2020 13712
    ADDITIONAL FUNDING-Bioinformatics analysis PI The main aims of the Project Microbiome and metagenome analysis of data already generated by Alltech to understand the following three topics: (1) Bacterial uniformity (2) Diversity, functionality and pathogen resistance (3) Functional antimicrobial resistance 25/08/2020 26/08/2021 482059.9
    COVID19 sequencing epidemiology PI 01/05/2020 31/10/2020 0
    ANTIVERSA (Stage 2) PI 03/02/2020 02/12/2022 149862.7
    Genomics to Investigate Risks of Toxin-Producing Vibrio in Irish Shellfish PI 01/02/2020 31/10/2022 13000
    Analysis of antimicrobial resistance risk in private drinking water supplies (ref:2019-W-PhD-14) PI Co- fund 50:50. Fiona has confirmed the Human Health Institute will fund the MU 50 %. 01/10/2019 30/09/2023 192000
    Bioinformatics analysis PI 01/09/2019 31/08/2020 482059.9
    Cofund EPA Maynooth University PI Our EU Water JPI project (Stare) identified specific mobile antibiotic resistance (AR) genes and bacteria in the effluent of wastewater treatment plants (WWTPs) in Ireland and the EU. These AR genes pose a threat to the treatment of human and animal infections if they transfer to pathogenic bacteria as they confer resistance to a wide range of antibiotics. The objective of this proposal is to identify the capabilities of these AR mechanisms carried on mobile DNA (plasmids) to survive in downstream water when they are released from WWTPs. This will be achieved by characterising the genetic components of the collected AR plasmids, analysing the collected plasmids for their ability to survive in receiving water and under antibiotic pressure similar to that identified in the WWTP effluents and identifying the plasmids capable of surviving and transferring to both resident water bacteria and pathogenic bacteria. The potential applications of the research findings are to describe the plasmids and AR genes emerging from WWTPs, which pose the greatest risk to human and animal health and further dissemination in the environment. This data is vital, as AR is becoming more important in water regulation as an emerging contaminant and further in the future we will need to identify what needs to be measured as a risk and to enable risk assessment models to be developed. 07/01/2019 06/01/2023 208000
    Antimicrobial Resistance and the Environment – Sources, persistence, Transmission and risk management PI Consortium bid, led by NUIG. Large Project - 48 months - budget €649,999.70 (under maximum of €1 million). Antimicrobial resistance (AMR) is recognised as one the greatest threats to human health as acknowledged in a series of authoritative reports in Ireland and elsewhere. The EPA have published guidance to minimise the risk of contamination of groundwaters associated with landspreading of organic waste. This project aims to address some of these knowledge gaps. 31/03/2018 28/02/2022 35510
    INART: JPI AMR (Stage 2) PI 01/01/2018 31/12/2020 325441
    StARE: Stopping Antibiotic Resistance Evolution PI 149948.39
    PRAHAD: Prevalence and optimised detection of resistance to antibiotics vital for animal and human health PI 246937.18
    Tracking antibiotic resistance from environmental reservoirs to the food chain PI 113718
    EI Coordination Support PI 12/11/2018 11/08/2019 12060
    Antibiotic discovery in soil bacteria PI Characterising the inhibition profile of a novel antibacterial 16/07/2018 07/09/2018 2153
    Comparative risk of antimicrobial resistance transfer from poultry, pig and bovine manure to grassland PI 01/10/2017 31/10/2021 90000.04
    ABAWAVE: ADVANCED BIOTECHNOLOGY FOR INTENSIVE – FRESHWATER AQUACULTURE WASTEWATER REUSE (Stage 2) PI 06/04/2017 05/04/2019 147196.64
    Travel to conference of FP7 project Evotar 24th June PI 24/06/2015 27/06/2015 0
    Microbioexcellence PI 25/05/2015 17/08/2015 0
    Travel to Switzerland for partner search for H2020 proposal PI 28/02/2014 02/03/2014 0
    Investigation of hospital sanitary ware as reservoirs of persistent antimicrobial resistant pathogens and links to bloodstream infections: Implications for infection prevention and control PI 03/12/2022 31/01/2027 401221.93
    JAMRAI2 - AMR surveillance One Health across Europe PI 01/01/2024 31/12/2027 161639.34
    Development of novel antibacterial agents PI Due to COVID-19 this project is deferred until summer 2021. This proposal will be submitted by MUHAMMUD ADIL 08/06/2021 03/08/2021 2400
    Additional funds_Extension 4- Alltech CRA_2019 PI 25/08/2023 26/08/2024 482059.9
    Artificial Animal Microbiome PI 14/02/2022 13/05/2022 19474
    Multi plasmid infection dynamics PI 26/02/2024 25/02/2026 15719
    NewResGenes - Informing genomic surveillance by uncovering, phenotyping and prioritising resistance genes to new antibiotics PI 01/06/2024 30/05/2027 241762
    Additional funds_Extension 3- Alltech CRA_2019 PI 26/08/2022 25/08/2023 482059.9
    A nationwide analysis of antimicrobial resistance in soil to bridge the gaps in data present in these environments. PI In collaboration with the ongoing DAFM nationwide survey of soils this project will investigate antimicrobial resistance (AMR) genes, their relative abundances and the microbial biodiversity of soils across Ireland. In addition, the genomes of ESBL Escherichia coli isolated by the DAFM survey will be sequenced. The data analysis will statistically analyse the AMR, microbial diversity and the soil characteristics to identify the soil characteristics associated with both high and low AMR content across Ireland. 03/01/2023 02/01/2027 524200.5
    Targeting antimicrobial resistance plasmids to resurrect antimicrobial therapies PI 01/12/2021 30/11/2026 1195039
    “Effects of Dietary Components on Antibiotic Resistance Using Mechanistic and Plasmid Based Studies" PI 194415
    SoilSynbiotics – Development of Synbiotics for enhancing the soil microbiome PI 01/04/2022 31/03/2025 246000
    Additional funds_Extension 2- Alltech CRA_2019 PI 26/08/2021 25/08/2022 482059.9

    Post Doctoral Fellows / Research Team

    Researcher Name Project Funding Body
    Emma Rossiter Linking Antimicrobial resistance and microbial diversity in soil and water
    Aidan O'Flaherty Advanced Biotechnology for Intensive Freshwater Aquaculture Wastewater reuse.
    Fiona Walsh Comparative risk of antimicrobial resistance transfer from poultry, pig and bovine manure to grassland
    Thi Thuy Do INART
    Dean Frawley SFI Frontiers for the Future Programme Award “Targeting antimicrobial resistance plasmids to resurrect antimicrobial therapies”
    Sarah Delaney Yeast wall components as inhibitors of antibiotic resistance transfer in the poultry gut microbiome
    Monika Subanovic SFI Frontiers for the Future Programme Award “Targeting antimicrobial resistance plasmids to resurrect antimicrobial therapies”
    Robert Leigh Metagenomic analysis of the impact of alternatives to antimicrobials on animal gut
    Aoife Joyce NFP72 Tracking antibiotic resistance from environmental reservoirs to the food chain

    Book Chapter

    Year Publication
    2019 Delaney S; Murphy R; Walsh F; (2019) 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples' In: Methods Mol Biol. Switzerland : Springer Nature. [DOI]
    2019 Delaney, S; Murphy, R; Walsh, F (2019) 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples' In: MICROBIAL TRANSPOSON MUTAGENESIS: PROTOCOLS AND APPLICATIONS. TOTOWA : HUMANA PRESS INC. [DOI]
    2017 Do T.; Murphy S.; Walsh F. (2017) 'Antibiotic Resistance and Wastewater Treatment Process' In: Antimicrobial Resistance in Wastewater Treatment Processes. [DOI]
    2017 Walsh F. (2017) 'Functional metagenomics and antimicrobial resistance' In: Functional Metagenomics: Tools and Applications. [DOI]
    2019 Delaney, S.; Murphy, R.; Walsh, F. (2019) 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples' In: Methods in Molecular Biology. [Link] [DOI]

    Edited Book

    Year Publication
    2015 Fiona Walsh (Ed.). (2015) The Multiple Roles of Antibiotics and Antibiotic Resistance in Nature. Switzerland: Frontiers in Microbiology, [DOI]

    Conference Contribution

    Year Publication
    2020 Do TT, Burgess K, Brennan F, Walsh F (2020) Effect of storage and composting on bacterial abundance in the pig manure Microbiology Society Annual Conference Scotland, .
    2020 Do TT, Burgess K, Brennan F, Walsh F. (2020) Bacterial abundance during storage and composting processes of the pig manure One Health EJP ASM Czech Republic, .
    2020 Do TT, Murphy S, Burgess K, Brennan F, Walsh F (2020) The effect of manure treatments on bacterial community in manure and on grassland ISME Finland, .
    2019 Do TT, O’Flaherty A, Walsh F (2019) Occurrence of extended-spectrum β-lactamase (ESBL)/AmpC producing bacteria in wastewater treatment plant effluent Microbiology Society Annual Conference Belfast, Northern Ireland, .
    2019 Do TT, O’Flaherty A, Walsh F (2019) Extended-spectrum β-lactamase (ESBL) producing bacteria in wastewater treatment plant effluent One Health EJP ASM Ireland, .
    2019 Do TT, Dugdale A, Collins G, Hayes N, Burgess C, Brennan F, Walsh F. (2019) Identification of antibiotic resistant bacteria in pig slurry Food Science Conference (FSAI) Ireland, .
    2018 Do TT, Delaney S, Walsh F (2018) The diversity of microbiome composition of wastewater treatment plant effluent Microbiology Society Annual Conference Birmingham, England, .
    2018 Do TT, Walsh F (2018) Stopping Antibiotic Resistance Evolution in the Environment (StARE) EPA-HSE Environment, Health & Wellbeing Conference Ireland, .
    2017 Do TT, Walsh F (2017) The antibiotic susceptibility of faecal coliforms isolated from wastewater plant effluent Microbiology Society Focused Meeting 2017-Irish Division: Antimicrobial Resistance and One Health Ireland, .
    2017 Do TT, Walsh F (2017) Identification of novel plasmid mediated colistin resistance in wastewater treatment plant effluent ECCMID Vienna, Austria, .
    2017 Do TT, Walsh F (2017) Antibiotic resistance prevalence of Pseudomonas spp. and identification of metallo-β-lactamase producing Pseudomonas. spp. in wastewater treatment plant effluent ARAE Germany, .
    2017 Do TT, Walsh F (2017) Characterization of multidrug resistance plasmids conferring resistance to colistin in wastewater treatment plant effluent Microbiology Society Annual Conference Edinburgh, Scotland, .
    2016 Do TT, Walsh F (2016) . Characterization of antibiotic resistant bacteria and detection of multi-drug resistance plasmids in wastewater treatment plant effluent in Ireland Microbiology Society Annual Conference Liverpool, England, .
    2016 Do TT, Walsh F (2016) Microbiome composition of wastewater treatment plant effluents in spring and autumn Microbiology Society Focused Meeting 2016 –Irish Division Ireland, .
    2016 Do TT, Poster FJ, Walsh F (2016) Antibiotic resistance in treated wastewater: the presence of antibiotic resistant bacteria and possibility of antibiotic resistance dissemination from WWTPs in Ireland Antibiotic resistance in treated wastewater: the presence of antibiotic resistant bacteria and possibility of antibiotic resistance dissemination from WWTPs in Ireland Ireland, .

    Peer Reviewed Journal

    Year Publication
    2023 Do TT; Smyth C; Crispie F; Burgess C; Brennan F; Walsh F; (2023) 'Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil'. Science of the Total Environment, 857 (Pt 1). [DOI] [Full-Text]
    2022 Leigh RJ; Corrigan A; Murphy RA; Walsh F; (2022) 'Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota'. Animal Microbiome, 4 (1). [DOI] [Full-Text]
    2022 Smyth C.; Leigh R.J.; Delaney S.; Murphy R.A.; Walsh F. (2022) 'Shooting hoops: globetrotting plasmids spreading more than just antimicrobial resistance genes across One Health'. Microbial Genomics, 8 (8). [DOI] [Full-Text]
    2022 Leigh R.J.; McKenna C.; McWade R.; Lynch B.; Walsh F. (2022) 'Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals'. Journal of Medical Microbiology, 71 (10). [DOI] [Full-Text]
    2022 Do T.T.; Nolan S.; Hayes N.; O'Flaherty V.; Burgess C.; Brennan F.; Walsh F. (2022) 'Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion'. Environmental Pollution, 305 . [DOI] [Full-Text]
    2021 Muna F Anjum, Heike Schmitt, Stefan Börjesson, Thomas U Berendonk, Fiona Walsh, WAWES network (2021) 'The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment'. Current Opinion in Microbiology, . [DOI] [Full-Text]
    2021 Margalit A; Carolan JC; Walsh F; (2021) 'Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin'. Journal of Global Antimicrobial Resistance, . [DOI] [Full-Text]
    2021 Gekenidis M.T.; Walsh F.; Drissner D. (2021) 'Tracing antibiotic resistance genes along the irrigation water chain to chive: Does tap or surface water make a difference?'. Journal of Antibiotics, 10 (9). [DOI] [Full-Text]
    2021 Delaney S.; Do T.T.; Corrigan A.; Murphy R.; Walsh F. (2021) 'Investigation into the effect of mannan-rich fraction supplementation on the metagenome of broiler chickens'. Microbial Genomics, 7 (7). [DOI] [Full-Text]
    2021 Funk T.; Pharris A.; Spiteri G.; Bundle N.; Melidou A.; Carr M.; Gonzalez G.; Garcia-Leon A.; Crispie F.; O’Connor L.; Murphy N.; Mossong J.; Vergison A.; Wienecke-Baldacchino A.K.; Abdelrahman T.; Riccardo F.; Stefanelli P.; Di Martino A.; Bella A.; Lo Presti A.; Casaca P.; Moreno J.; Borges V.; Isidro J.; Ferreira R.; Gomes J.P.; Dotsenko L.; Suija H.; Epstein J.; Sadikova O.; Sepp H.; Ikonen N.; Savolainen-Kopra C.; Blomqvist S.; Möttönen T.; Helve O.; Gomes-Dias J.; Adlhoch C.; Macori G.; Russell L.; Yandle Z.; Bennett C.; O'Byrne E.; Murphy A.; Tuite G.; Conroy A.; Duffy M.; Morley U.; Keoghan B.; Ford I.; Kennedy M.; McDonnell S.; Flynn A.; Clarke A.; Crowley A.; Martin C.; Kelly E.; Foxton J.; Hare D.; Dunford L.; Connell J.; Moran J.; Dean J.; Fanning S.; Rajan L.; De Gascun C.; Kenny J.; Cotter P.; Walsh C.; Lawton E.; Fitzpatrick A.; Mullins E.; Della Bartola M.; McCabe M.; Stapleton P.; Meaney C.; Fanning L.; Prentice M.; MacSharry J.; Dempsey C.; Mallon P.; Leon A.; Chaturvedi A.; Coughlan S.; McAndrew G.; Reddington K.; Walsh F.; Fitzpatrick D.; Smyth C.; O’Dwyer T.; Chambers T.; Clarke L.; Jebb D.; Klopp J.; Kavanagh D.; Haslam K.; Buckley P.; Lemass K.; Fitzpatrick F.; Burns K. (2021) 'Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021'. Eurosurveillance, 26 (16). [DOI] [Full-Text]
    2020 Smyth C; O'Flaherty A; Walsh F; Do TT; (2020) 'Antibiotic resistant and extended-spectrum β-lactamase producing faecal coliforms in wastewater treatment plant effluent'. Environmental Pollution, 262 . [DOI] [Full-Text]
    2020 Purchase, D; Abbasi, G; Bisschop, L; Chatterjee, D; Ekberg, C; Ermolin, M; Fedotov, P; Garelick, H; Isimekhai, K; Kandile, NG; Lundstrom, M; Matharu, A; Miller, BW; Pineda, A; Popoola, OE; Retegan, T; Ruedel, H; Serpe, A; Sheva, Y; Surati, KR; Walsh, F; Wilson, BP; Wong, MH (2020) 'Global occurrence, chemical properties, and ecological impacts of e-wastes (IUPAC Technical Report)'. Pure and Applied Chemistry, 92 :1733-1767. [DOI] [Full-Text]
    2020 Eissenberger K.; Drissner D.; Walsh F.; Weiss A.; Schmidt H. (2020) 'Plant variety and soil type influence Escherichia coli O104:H4 strain C227/11ϕcu adherence to and internalization into the roots of lettuce plants'. Food Microbiology, 86 . [DOI] [Full-Text]
    2020 Rodriguez-Mozaz S.; Vaz-Moreira I.; Varela Della Giustina S.; Llorca M.; Barceló D.; Schubert S.; Berendonk T.U.; Michael-Kordatou I.; Fatta-Kassinos D.; Martinez J.L.; Elpers C.; Henriques I.; Jaeger T.; Schwartz T.; Paulshus E.; O'Sullivan K.; Pärnänen K.M.M.; Virta M.; Do T.T.; Walsh F.; Manaia C.M. (2020) 'Antibiotic residues in final effluents of European wastewater treatment plants and their impact on the aquatic environment'. Environmental International, 140 . [DOI] [Full-Text]
    2020 Gekenidis, MT; Rigotti, S; Hummerjohann, J; Walsh, F; Drissner, D (2020) 'Long-Term Persistence of bla(CTX-M-15) in Soil and Lettuce after Introducing Extended-Spectrum beta-Lactamase (ESBL)-Producing Escherichia coli via Manure or Water'. Microorganisms, 8 . [DOI] [Full-Text]
    2019 Pärnänen KMM; Narciso-da-Rocha C; Kneis D; Berendonk TU; Cacace D; Do TT; Elpers C; Fatta-Kassinos D; Henriques I; Jaeger T; Karkman A; Martinez JL; Michael SG; Michael-Kordatou I; O'Sullivan K; Rodriguez-Mozaz S; Schwartz T; Sheng H; Sørum H; Stedtfeld RD; Tiedje JM; Giustina SVD; Walsh F; Vaz-Moreira I; Virta M; Manaia CM; (2019) 'Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence'. Science Advances, 5 (3). [DOI] [Full-Text]
    2019 Joyce A; McCarthy CGP; Murphy S; Walsh F; (2019) 'Antibiotic resistomes of healthy pig faecal metagenomes'. Microbial Genomics, 5 (5). [DOI] [Full-Text]
    2019 T T Do, S Delaney, F Walsh (2019) '16S rRNA based bacterial community structure of wastewater treatment plant effluents'. Fems Microbiology Letters, . [DOI] [Full-Text]
    2019 Tyrrell C; Burgess CM; Brennan FP; Walsh F; (2019) 'Antibiotic resistance in grass and soil'. Biochemical Society Transactions, 47 (1). [DOI]
    2019 Delaney S.; Murphy R.; Walsh F. (2019) 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples'. Methods in molecular biology (Clifton, N.J.), 2016 :151-157. [DOI]
    2018 Gekenidis MT; Schöner U; von Ah U; Schmelcher M; Walsh F; Drissner D; (2018) 'Tracing back multidrug-resistant bacteria in fresh herb production: from chive to source through the irrigation water chain'. FEMS MICROBIOLOGY ECOLOGY, . [DOI] [Full-Text]
    2018 Gekenidis MT; Qi W; Hummerjohann J; Zbinden R; Walsh F; Drissner D; (2018) 'Antibiotic-resistant indicator bacteria in irrigation water: High prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli'. PLoS ONE, 13 (11). [DOI] [Full-Text]
    2018 Delaney S.; Murphy R.; Walsh F. (2018) 'A comparison of methods for the extraction of plasmids capable of conferring antibiotic resistance in a human pathogen from complex broiler cecal samples'. Frontiers in Microbiology, 9 (AUG). [DOI] [Full-Text]
    2018 Walsh F.; Richards P. (2018) 'Antimicrobial resistance and one health'. Microbiology Today, 45 (1):38-39. [Full-Text]
    2017 Thi Thuy Do, Javier Tamames, Robert 
Stedtfeld, Xueping 
Guo, Sinead Murphy, James Tiedje, Fiona
 Walsh (2017) 'Antibiotic Resistance Gene Detection in the Microbiome Context'. Microbial Drug Resistance, . [DOI] [Full-Text]
    2016 Fitzpatrick D; Walsh F; (2016) 'Antibiotic resistance genes across a wide variety of metagenomes'. FEMS MICROBIOLOGY ECOLOGY, 92 (2). [DOI] [Full-Text]
    2016 Thanner S.; Drissner D.; Walsh F. (2016) 'Antimicrobial resistance in agriculture'. mBio, 7 (2). [DOI] [Full-Text]
    2015 Fiona Fouhy, Catherine Stanton, Paul David Cotter, Colin Hill, Dr Fiona Walsh (2015) 'Proteomics as the final step in the functional metagenomics study of antimicrobial resistance'. 3 . [DOI] [Full-Text]
    2015 Dunbar J.; Zarelli M.; Martin S.; Gandola R.; Kavanagh K.; Walsh F.; Rivas J. (2015) 'Trunk vertebrae osteomyelitis in a spectacled caiman (Caiman crocodilus)'. Herpetological Bulletin, (134):15-18. [Full-Text]
    2015 Weiss, A; Scheller, F; Oggenfuss, M; Walsh, F; Frey, JE; Drissner, D; Schmidt, H (2015) 'ANALYSIS OF THE BACTERIAL EPIPHYTIC MICROBIOTA OF OAK LEAF LETTUCE WITH 16S RIBOSOMAL RNA GENE ANALYSIS'. Journal Of Microbiology Biotechnology And Food Sciences, 5 :271-276. [DOI] [Full-Text]
    2015 Berendonk, TU; Manaia, CM; Merlin, C; Fatta-Kassinos, D; Cytryn, E; Walsh, F; Burgmann, H; Sorum, H; Norstrom, M; Pons, MN; Kreuzinger, N; Huovinen, P; Stefani, S; Schwartz, T; Kisand, V; Baquero, F; Martinez, JL (2015) 'Tackling antibiotic resistance: the environmental framework'. Nature Reviews Microbiology, 13 :310-317. [DOI] [Full-Text]
    2014 Walsh F.; Pelludat C.; Duffy B.; Smith D.; Owens S.; Frey J.; Holliger E. (2014) 'Impact of streptomycin applications on antibiotic resistance in apple orchards | Einfluss von streptomycin in apfelanlagen auf antibiotika-resistenzen in der umwelt'. Agrarforschung Schweiz, 5 (7-8):300-305. [Full-Text]
    2014 B. Duffy, E. Holliger, Dr Fiona Walsh (2014) 'Streptomycin use in apple orchards did not increase the abundance of mobile resistance genes'. Fems Microbiology Letters, 350 :180-189. [Full-Text]
    2014 Dr Fiona Walsh, C. Pelludat, B. Duffy, D.P. Smith, S.M. Owens, J.E. Frey, E. Holliger. (2014) 'Einfluss von Streptomycin in Apfelanlagen auf Antibiotika-Resistenzen in der Umwelt. Agrarforschung Schweiz'. To be added, 5 :300-305. [Full-Text]
    2014 J.A. Bunge, A. Willis, F. Walsh (2014) 'Estimating the Number of Species in Microbial Diversity Studies'. 1 :427-445. [Full-Text]
    2014 Dr Fiona Walsh, D.P. Smith, S.M. Owens, B. Duffy, J.E. Frey (2014) 'Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities'. 4 . [Full-Text]
    2013 Dr Fiona Walsh (2013) 'Investigating antibiotic resistance in non-clinical environments'. Frontiers in Microbiology, . [DOI] [Full-Text]
    2013 Dr Fiona Walsh (2013) 'A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota'. Frontiers in Microbiology, 4 . [DOI] [Full-Text]
    2013 Dr Fiona Walsh, SG Amyes, B Duffy (2013) 'Challenging the concept of bacteria subsisting on antibiotics'. International Journal of Antimicrobial Agents, 41 :558-563. [Full-Text]
    2013 Dr Fiona Walsh, B. Duffy (2013) 'The culturable soil antibiotic resistome: A community of multi-drug resistant bacteria'. PLoS ONE, 8 . [Full-Text]
    2012 M. Popowska, M. Rzeczycka, A. Miernik, A. Krawczyk-Balska, F. Walsh, B. Duffy (2012) 'Influence of soil use on prevalence of tetracycline, streptomycin, and erythromycin resistance and associated resistance genes'. Antimicrobial Agents and Chemotherapy, 56 :1434-1443. [DOI] [Full-Text]
    2012 Dr Fiona Walsh, TR Rogers (2012) 'Comparison of plasmid-mediated quinolone resistance and extended spectrum beta-lactamases in 3rd generation cephalosporin resistant Enterobacteriaceae from four Irish hospitals'. Journal of Medical Microbiology, 61 :142-147. [DOI] [Full-Text]
    2011 Dr Fiona Walsh, A Ingenfeld, M. Zampicolli, M. Hilber-Bodmer, J. E. Frey, B. Duffy. (2011) 'Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems'. Journal of Microbiological Methods, 86 :150-155. [DOI] [Full-Text]
    2011 B. Duffy, F. Walsh, C. Pelludat, E. Holliger, J. Ouvelet, F. Widmer. (2011) 'Environmental monitoring of antibiotic resistance and impact of streptomycin use on orchard bacterial communities'. Acta Horticulturae, 3 :483-488.
    2010 F. Walsh, N. M. Cooke, S.G. Smith, G. P. Moran, F. J. Cooke, A. Ivens, J. Wain, T. R. Rogers. (2010) 'Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae'. International Journal of Antimicrobial Agents, 35 :593-598. [DOI] [Full-Text]
    2009 T.W. Boo, F. Walsh, B. Crowley. (2009) 'Molecular characterization of carbapenem-resistant Acinetobacter species in an Irish university hospital: predominance of Acinetobacter genomic species 3'. Journal of Medical Microbiology, 58 :209-216. [DOI] [Full-Text]
    2008 F. Walsh, T. R. Rogers. (2008) 'Detection of blaVIM-2 carbapenemase in Pseudomonas aeruginosa in Ireland. Journal of Antimicrobial Chemotherapy'. Journal of Antimicrobial Chemotherapy, 61 :219-229. [Full-Text]
    2008 C. Roche, T.W. Boo, F. Walsh, B. Crowley. (2008) 'Detection and molecular characterisation of plasmidic AmpC β-lactamases in Klebsiella pneumoniae from a tertiary care hospital in Dublin, Ireland'. Clinical Microbiology and Infection, 14 :616-618. [Full-Text]
    2007 Walsh F; (2007) 'Doripenem: A new carbapenem antibiotic a review of comparative antimicrobial and bactericidal activities'. Therapeutics and Clinical Risk Management, 3 (5). [Full-Text]
    2007 Amyes SG; Walsh FM; Bradley JS; (2007) 'Best in class: a good principle for antibiotic usage to limit resistance development?'. Journal of Antimicrobial Chemotherapy, 59 (5). [DOI] [Full-Text]
    2007 F. Walsh and S.G.B. Amyes. (2007) 'Carbapenem resistance in clinical isolates of Pseudomonas aeruginosa'. 19 :376-381.
    2007 F. Walsh, S. Bracher, P. Turner, S. Amyes. (2007) 'Preferential selection of IMP and VIM metallo-β-lactamases by imipenem in Pseudomonas aeruginosa'. Journal of Chemotherapy, 53 :407-409. [Full-Text]
    2006 T. W. Boo, F. Walsh, B. Crowley. (2006) 'First report of OXA-23 carbapenemase in clinical isolates of Acinetobacter species in the Irish Republic'. Journal of Antimicrobial Chemotherapy, 58 :1101-1102. [Full-Text]
    2005 F. Walsh, S. Bracher, P. Turner, S. G. Amyes. (2005) 'Epidemiological analysis of carbapenem-sensitive and -resistant Pseudomonas aeruginosa'. Journal of Hospital Infection, 60 :240-244. [Full-Text]
    2004 .F. Walsh, F. Carnegy, J. Willcock, S. Amyes. (2004) 'Comparative in vitro activity of telithromycin against macrolide-resistant and -susceptible Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae'. Journal of Antimicrobial Chemotherapy, 53 :793-796. [Full-Text]
    2004 Walsh FM; Amyes SG; (2004) 'Microbiology and drug resistance mechanisms of fully resistant pathogens'. Current Opinion in Microbiology, 7 (5). [DOI] [Full-Text]
    2003 F. Walsh, A. K. Amyes, S. G. Amyes. (2003) 'The in vitro effects of faropenem on lower respiratory tract pathogens isolated in the United Kingdom'. International Journal of Antimicrobial Agents, 21 :581-584. [Full-Text]
    2003 F. Walsh, J. Willcock, S. Amyes. (2003) 'High-level telithromycin resistance in laboratory-generated mutants of Streptococcus pneumoniae'. Journal of Antimicrobial Chemotherapy, 52 :345-353. [Full-Text]
    2002 F. Walsh, J. Willcock, S. G. Amyes. (2002) 'Culturing Chlamydophila pneumoniae'. 14 :312-313. [Full-Text]
    2024 Eimear K. Ryan,* Christy Clutter,†,‡ Conor De Barra,* Benjamin J. Jenkins,§ Simon O’Shaughnessy,{ Odhra ́n K. Ryan,*,|| Chloe McKenna,* Helen M. Heneghan,|| Fiona Walsh,* David K. Finlay,{,# Linda V. Sinclair,** Nicholas Jones,§ Daniel T. Leung,†,‡ Donal O’Shea,*,|| and Andrew E. Hogan* (2024) 'Iron Is Critical for Mucosal-Associated Invariant T Cell Metabolism and Effector Functions'. Journal of Immunology, . [DOI] [Full-Text]
    2024 Leigh, R.J.; Corrigan, A.; Murphy, R.A.; Walsh, F. (2024) 'Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance'. Animal Microbiome, 6 . [Link] [DOI]
    2024 Klümper, U.; Gionchetta, G.; Catão, E.; Bellanger, X.; Dielacher, I.; Elena, A.X.; Fang, P.; Galazka, S.; Goryluk-Salmonowicz, A.; Kneis, D.; Okoroafor, U.; Radu, E.; Szadziul, M.; Szekeres, E.; Teban-Man, A.; Coman, C.; Kreuzinger, N.; Popowska, M.; Vierheilig, J.; Walsh, F.; Woegerbauer, M.; Bürgmann, H.; Merlin, C.; Berendonk, T.U. (2024) 'Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation'. Communications Biology, 7 . [Link] [DOI]
    2023 Tyrrell, C.; Do, T.T.; Leigh, R.J.; Burgess, C.M.; Brennan, F.P.; Walsh, F. (2023) 'Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland'. Science of the Total Environment, 886 . [Link] [DOI] [Full-Text]
    2023 Corrigan, A.; Leigh, R.J.; Walsh, F.; Murphy, R. (2023) 'Microbial community diversity and structure in the cecum of laying hens with and without mannan-rich fraction supplementation'. Journal of Applied Poultry Research, 32 . [Link] [DOI] [Full-Text]
    2023 Yin, X.; Chen, X.; Jiang, X.T.; Yang, Y.; Li, B.; Shum, M.H.H.; Lam, T.T.Y.; Leung, G.M.; Rose, J.; Sanchez-Cid, C.; Vogel, T.M.; Walsh, F.; Berendonk, T.U.; Midega, J.; Uchea, C.; Frigon, D.; Wright, G.D.; Bezuidenhout, C.; Picão, R.C.; Ahammad, S.Z.; Nielsen, P.H.; Hugenholtz, P.; Ashbolt, N.J.; Corno, G.; Fatta-Kassinos, D.; Bürgmann, H.; Schmitt, H.; Cha, C.J.; Pruden, A.; Smalla, K.; Cytryn, E.; Zhang, Y.; Yang, M.; Zhu, Y.G.; Dechesne, A.; Smets, B.F.; Graham, D.W.; Gillings, M.R.; Gaze, W.H.; Manaia, C.M.; Van Loosdrecht, M.C.M.; Alvarez, P.J.J.; Blaser, M.J.; Tiedje, J.M.; Topp, E.; Zhang, T. (2023) 'Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples'. Environmental Science and Technology, . [Link] [DOI]
    2023 Corrigan A., Leigh R.J., Walsh F., and Murphy R.A. (2023) 'Microbial community diversity and structure in the cecum of laying hens with and without mannan-rich fraction supplementation'. Journal of Applied Poultry Research, . https://doi.org/10.1016/j.japr.2023.100342 [Full-Text]
    2023 Mateo-Estrada, V.; Tyrrell, C.; Evans, B.A.; Aguilar-Vera, A.; Drissner, D.; Castillo-Ramirez, S.; Walsh, F. (2023) 'Acinetobacter baumannii from grass: novel but non-resistant clones'. Microbial Genomics, 9 . [Link] [DOI]
    2021 Leigh R.J., McKenna C., McWade R., Lynch B., Walsh F (2021) 'Comparative genomics and pangenomics of vancomycin resistant and susceptible Enterococcus faecium from Irish hospitals across 20 years'. Biorxiv : The Preprint Server For Biology, . https://doi.org/10.1101/2021.11.22.469549 [Full-Text]
    2016 Fitzpatrick D, Walsh F (2016) 'Antibiotic resistance genes across a wide variety of metagenomes'. FEMS MICROBIOLOGY ECOLOGY, 2016 Jan 5 [Epub ahead of print] .

    Editorial

    Year Publication
    2013 Walsh, F (2013) The multiple roles of antibiotics and antibiotic resistance in nature. LAUSANNE: [Editorial] [DOI]
    2007 Amyes S.; Walsh F.; Bradley J. (2007) Best in class: A good principle for antibiotic usage to limit resistance development?. [Editorial] [DOI]

    Reviews

    Year Publication
    2022 Alawi M.; Torrijos T.V.; Walsh F. (2022) Plasmid-mediated antimicrobial resistance in drinking water. [Reviews] [DOI]
    2019 Tyrrell C.; Burgess C.; Brennan F.; Walsh F. (2019) Antibiotic resistance in grass and soil. [Reviews] [DOI]
    2018 Karkman, A; Do, TT; Walsh, F; Virta, MPJ (2018) Antibiotic-Resistance Genes in Waste Water. OXFORD: [Reviews] [DOI] [Full-Text]
    2004 Walsh F.; Amyes S. (2004) Microbiology and drug resistance mechanisms of fully resistant pathogens. [Reviews] [DOI]

    Other Publication

    Year Publication
    2024 Leigh, R.J.; Corrigan, A.; Murphy, R.A.; Taylor-Pickard, J.; Moran, C.A.; Walsh, F. (2024) Correction to: Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance (Animal Microbiome, (2024), 6, 1, (9), 10.1186/s42523-024-00295-7). [Link] [DOI]
    Certain data included herein are derived from the © Web of Science (2024) of Clarivate. All rights reserved.

    Professional Associations

    Description Function From / To
    ECSMID, EFWISG executive committee chairperson Chairperson 01/04/2020 - 31/03/2022
    Food and Agriculture Organization (FAO) of the United Nations Expert committee member on AMR in Food, crops and the environment 01/01/2017 - 31/12/2022
    Water JPI Knowledge Hub Member 01/01/2018 - 31/12/2020
    Food and Agriculture Organization (FAO) of the United Nations Expert committee member on AMR in Horticulture 02/10/2017 - 21/03/2018
    Microbiology Society Irish division committee member 03/10/2016 - 21/03/2018
    Maynooth University BSRESC ethics committee Chair & member 03/10/2016 - 21/03/2018
    ESSEM COST Action ES1403 Short term scientific missions (STSM) coordinator, steering committee & management committee member 01/10/2014 - 21/03/2018

    Honors and Awards

    Date Title Awarding Body
    01/11/2020 Faculty of Science and Engineering Research Achievement Award, Maynooth University Maynooth University
    01/01/2014 American Society for Microbiology (ASM) outstanding service award American Society for Microbiology
    01/01/2013 Publication prize Agroscope Swiss Federal Department of Agriculture
    01/01/2012 EU COST ESSEM ESR Award
    01/01/2008 Wiser Post-Doctoral Researcher Award
    01/01/2003 The Wellcome Trust VIP fund award
    01/01/2006 Health Research Board Post-Doctoral Research Personal Fellow
    01/09/2022 Ranked in the top 2% of scientists globally Clarivate
    01/09/2022 Top environmental microbiology researcher in Ireland Clarivate
    01/09/2020 Ranked in the top 2% of scientists globally Clarivate

    Committees

    Committee Function From / To
    ESSEM COST Action ES1403 New and emerging challenges and opportunities in wastewater reuse (NEREUS) Short term scientific missions (STSM) coordinator, steering committee & management committee member. 01/09/2014 - 30/08/2018
    Member of the One Health EJP mirror group (DAFM) Member -
    Irish division of the Microbiology Society Committee member 01/09/2016 - 30/08/2019
    Soil Mission mirror group (DAFM) Member -
    Water JPI Knowledge Hub Member -
    Maynooth University BSRESC ethics committee Chair & member 01/09/2016 - 30/08/2019
    Food Safety Authority of Ireland Biological Safety subcommittee Expert -
    Kathleen Lonsdale Human Health Institute steering committee (MU) Member -
    AMR One Health Thematic Network (Department of Agriculture Food and the Marine (DAFM)) Member -
    Working Group on Open Access and Open Scholarship Member 01/09/2021 - 31/08/2022
    Faculty of Science & Engineering Research Committee, Maynooth University Member -
    Department of Biology, Research Committee, Maynooth University Chair -

    Teaching Interests

    I teach courses on environmental microbiology e.g. BI207, which describes the role of the environment in disease transmission and how diseases emerge from the environment or animal reservoirs. I also teach practical courses on molecular biology and bacterial sequencing. In the 4th year of the biology degree students can study a module on antimicrobial action and antimicrobial resistance. During this module we explore how antimicrobials inhibit bacteria and the many ways in which bacteria can evade, avoid, destroy or change antimicrobials to become resistant.

    Current Students

    Student Name Degree Supervision
    MR G.C. DILLON RESEARCH PH.D. (10)
    MS S.A. O'SHEA RESEARCH PH.D. (10)
    MARWA ALAWI RESEARCH PH.D. (10)
    MS C. MC KENNA RESEARCH PH.D. (10)
    MS S. CARTER RESEARCH MASTERS (9)
    MR D.N. TANSEY RESEARCH PH.D. (10)
    MS E.P. KILCOYNE RESEARCH MASTERS (9)
    CIAN DAIRE SMYTH RESEARCH PH.D. (10)

    Recent Students

    Graduation date Name Degree
    2011 Sarah Molan PhD
    2022 Ciara Tyrrell PhD
    2024 Marwa alawi PhD
    2024 Cian Smyth PhD
    2023 Katie Boyle PhD
    2019 Sarah Delaney PhD

    External Collaborators

    Name Role Country
    Prof Célia Manaia. Universidade Católica Portuguesa EU Water JPI project
    Prof Laura JV Piddock. Birmingham University EU ERA-Net project
    Prof Martin Ackermann. ETH Zurich Bilateral
    Prof Laurent Poirel. University Fribourg EU project
    Norweigan University of Life Sciences Consortium lead Norway
    University of Lausanne Switzerland
    Dr Juerg Frey. Agroscope Metagenomics