Fiona Walsh

Prof Fiona Walsh

Biology, Human Health Institute

Professor

Location Biosciences & Electronic Engineering Facility

Room B1.24

Phone (01) 474 7246

Email fiona.walsh@mu.ie

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

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

Publications

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]

Professional

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

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

Collaborators

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