Dr Fiona Walsh

Biology, Human Health Institute

Lecturer
Assistant 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 Projects

  Project Role Funding Body / Program Description Start Date End Date Award (€)
“Effects of Dietary Components on Antibiotic Resistance Using Mechanistic and Plasmid Based Studies" PI Alltech / 2266258 194415
StARE: Stopping Antibiotic Resistance Evolution PI EU Horizon 2020 / 2265111 149948.39
PRAHAD: Prevalence and optimised detection of resistance to antibiotics vital for animal and human health PI Department of Agriculture, Fisheries and Food (Ireland) / DAFM / 2265108 246937.18
Tracking antibiotic resistance from environmental reservoirs to the food chain PI Swiss National Science Foundation / 2266426 113718
Analysis of antimicrobial resistance risk in private drinking water supplies (ref:2019-W-PhD-14) PI Environmental Protection Agency Ireland / EPA / 2263419 Co- fund 50:50. Fiona has confirmed the Human Health Institute will fund the MU 50 %. 01-OCT-19 30-SEP-23 192000
Bioinformatics analysis PI Alltech / 2373113 01-SEP-19 31-AUG-20 76259
Cofund EPA Maynooth University PI Environmental Protection Agency Ireland / EPA / 2263419 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-JAN-19 06-JAN-23 208000
EI Coordination Support PI Enterprise Ireland H2020 Support / 2322031 12-NOV-18 11-AUG-19 12060
Antibiotic discovery in soil bacteria PI Society for General Microbiology (SGM) / 2264251 Characterising the inhibition profile of a novel antibacterial 16-JUL-18 07-SEP-18 2153
Antimicrobial Resistance and the Environment – Sources, persistence, Transmission and risk management PI Environmental Protection Agency Ireland / EPA / 2263229 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-MAR-18 28-FEB-22 35510
INART: JPI AMR (Stage 2) PI European Union / EU / 2347313 01-JAN-18 31-DEC-20 325441
Comparative risk of antimicrobial resistance transfer from poultry, pig and bovine manure to grassland PI Teagasc / 2263388 01-OCT-17 31-OCT-21 88000
ABAWAVE: ADVANCED BIOTECHNOLOGY FOR INTENSIVE – FRESHWATER AQUACULTURE WASTEWATER REUSE (Stage 2) PI European Union / EU / 2265099 06-APR-17 05-APR-19 147196.64
Travel to conference of FP7 project Evotar 24th June PI EU Horizon 2020 National Support Network / 2265103 24-JUN-15 27-JUN-15
Microbioexcellence PI Enterprise Ireland / 2264718 25-MAY-15 17-AUG-15
Travel to Switzerland for partner search for H2020 proposal PI EU Horizon 2020 National Support Network / 2265103 28-FEB-14 02-MAR-14

Book Chapters

  Year Publication
2019 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples'
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] [Details]
2019 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples'
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] [Details]
2017 'Antibiotic Resistance and Wastewater Treatment Process'
Do T.;Murphy S.;Walsh F. (2017) 'Antibiotic Resistance and Wastewater Treatment Process' In: Antimicrobial Resistance in Wastewater Treatment Processes. [DOI] [Details]
2017 'Functional metagenomics and antimicrobial resistance'
Walsh F. (2017) 'Functional metagenomics and antimicrobial resistance' In: Functional Metagenomics: Tools and Applications. [DOI] [Details]

Edited Books

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

Peer Reviewed Journals

  Year Publication
2020 'Plant variety and soil type influence Escherichia coli O104:H4 strain C227/11ϕcu adherence to and internalization into the roots of lettuce plants'
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] [Details]
2019 'Transposon-Aided Capture of Antibiotic Resistance Plasmids from Complex Samples'
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] [Details]
2019 'Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence'
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] [Details]
2019 '16S rRNA based bacterial community structure of wastewater treatment plant effluents'
T T Do, S Delaney, F Walsh (2019) '16S rRNA based bacterial community structure of wastewater treatment plant effluents'. Fems Microbiology Letters, [DOI] [Details]
2019 'Antibiotic resistance in grass and soil'
Tyrrell C;Burgess CM;Brennan FP;Walsh F; (2019) 'Antibiotic resistance in grass and soil'. Biochemical Society Transactions, 47 (1) [DOI] [Details]
2019 'Antibiotic resistomes of healthy pig faecal metagenomes'
Joyce A;McCarthy CGP;Murphy S;Walsh F; (2019) 'Antibiotic resistomes of healthy pig faecal metagenomes'. Microbial Genomics, 5 (5) [DOI] [Details]
2018 'Antibiotic-resistant indicator bacteria in irrigation water: High prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli'
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] [Details]
2018 'Antimicrobial resistance and one health'
Walsh F.;Richards P. (2018) 'Antimicrobial resistance and one health'. Microbiology Today, 45 (1):38-39 [Details]
2018 'Antibiotic resistance genes in waste water'
Antti Karkman, Thi Thuy Do, Fiona Walsh, Marko PJ Virta (2018) 'Antibiotic resistance genes in waste water'. Trends in Microbiology, [IR Link] [Details]
2017 'Antibiotic Resistance Gene Detection in the Microbiome Context'
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] [IR Link] [Details]
2015 'Trunk vertebrae osteomyelitis in a spectacled caiman (Caiman crocodilus)'
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 [Details]
2015 'ANALYSIS OF THE BACTERIAL EPIPHYTIC MICROBIOTA OF OAK LEAF LETTUCE WITH 16S RIBOSOMAL RNA GENE ANALYSIS'
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] [Details]
2007 'Doripenem: A new carbapenem antibiotic a review of comparative antimicrobial and bactericidal activities'
Walsh F; (2007) 'Doripenem: A new carbapenem antibiotic a review of comparative antimicrobial and bactericidal activities'. Therapeutics and Clinical Risk Management, 3 (5) [Details]
2007 'Best in class: a good principle for antibiotic usage to limit resistance development?'
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] [Details]
2004 'Microbiology and drug resistance mechanisms of fully resistant pathogens'
Walsh FM;Amyes SG; (2004) 'Microbiology and drug resistance mechanisms of fully resistant pathogens'. Current Opinion in Microbiology, 7 (5) [DOI] [Details]
2018 'Tracing back multidrug-resistant bacteria in fresh herb production: from chive to source through the irrigation water chain'
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] [IR Link] [Details]
2018 'A comparison of methods for the extraction of plasmids capable of conferring antibiotic resistance in a human pathogen from complex broiler cecal samples'
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] [IR Link] [Details]
2016 'Antibiotic resistance genes across a wide variety of metagenomes'
Fitzpatrick D;Walsh F; (2016) 'Antibiotic resistance genes across a wide variety of metagenomes'. FEMS MICROBIOLOGY ECOLOGY, 92 (2) [DOI] [IR Link] [Details]
2015 'Tackling antibiotic resistance: the environmental framework'
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] [Details]
2013 'A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota'
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] [IR Link] [Details]
2013 'Investigating antibiotic resistance in non-clinical environments'
Dr Fiona Walsh (2013) 'Investigating antibiotic resistance in non-clinical environments'. Frontiers in Microbiology, [DOI] [Details]
2016 'Antimicrobial resistance in agriculture'
Thanner S.;Drissner D.;Walsh F. (2016) 'Antimicrobial resistance in agriculture'. mBio, 7 (2) [DOI] [IR Link] [Details]
2014 'Impact of streptomycin applications on antibiotic resistance in apple orchards | Einfluss von streptomycin in apfelanlagen auf antibiotika-resistenzen in der umwelt'
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 [IR Link] [Details]
2015 'Proteomics as the final step in the functional metagenomics study of antimicrobial resistance'
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] [IR Link] [Details]
2014 'Einfluss von Streptomycin in Apfelanlagen auf Antibiotika-Resistenzen in der Umwelt. Agrarforschung Schweiz'
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 [IR Link] [Details]
2014 'Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities'
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 [IR Link] [Details]
2014 'Streptomycin use in apple orchards did not increase the abundance of mobile resistance genes'
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 [IR Link] [Details]
2014 'Estimating the Number of Species in Microbial Diversity Studies'
J.A. Bunge, A. Willis, F. Walsh (2014) 'Estimating the Number of Species in Microbial Diversity Studies'. 1 :427-445 [Details]
2013 'The culturable soil antibiotic resistome: A community of multi-drug resistant bacteria'
Dr Fiona Walsh, B. Duffy (2013) 'The culturable soil antibiotic resistome: A community of multi-drug resistant bacteria'. PLoS ONE, 8 [IR Link] [Details]
2013 'Challenging the concept of bacteria subsisting on antibiotics'
Dr Fiona Walsh, SG Amyes, B Duffy (2013) 'Challenging the concept of bacteria subsisting on antibiotics'. INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, 41 :558-563 [IR Link] [Details]
2012 'Comparison of plasmid-mediated quinolone resistance and extended spectrum beta-lactamases in 3rd generation cephalosporin resistant Enterobacteriaceae from four Irish hospitals'
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] [IR Link] [Details]
2012 'Influence of soil use on prevalence of tetracycline, streptomycin, and erythromycin resistance and associated resistance genes'
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] [IR Link] [Details]
2011 'Environmental monitoring of antibiotic resistance and impact of streptomycin use on orchard bacterial communities'
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 [Details]
2011 'Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems'
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] [IR Link] [Details]
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'
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] [IR Link] [Details]
2009 'Molecular characterization of carbapenem-resistant Acinetobacter species in an Irish university hospital: predominance of Acinetobacter genomic species 3'
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] [IR Link] [Details]
2008 'Detection and molecular characterisation of plasmidic AmpC β-lactamases in Klebsiella pneumoniae from a tertiary care hospital in Dublin, Ireland'
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 [IR Link] [Details]
2008 'Detection of blaVIM-2 carbapenemase in Pseudomonas aeruginosa in Ireland. Journal of Antimicrobial Chemotherapy'
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 [IR Link] [Details]
2007 'Preferential selection of IMP and VIM metallo-β-lactamases by imipenem in Pseudomonas aeruginosa'
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 [Details]
2007 'Carbapenem resistance in clinical isolates of Pseudomonas aeruginosa'
F. Walsh and S.G.B. Amyes. (2007) 'Carbapenem resistance in clinical isolates of Pseudomonas aeruginosa'. 19 :376-381 [Details]
2006 'First report of OXA-23 carbapenemase in clinical isolates of Acinetobacter species in the Irish Republic'
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 [IR Link] [Details]
2005 'Epidemiological analysis of carbapenem-sensitive and -resistant Pseudomonas aeruginosa'
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 [IR Link] [Details]
2004 'Comparative in vitro activity of telithromycin against macrolide-resistant and -susceptible Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae'
.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 [IR Link] [Details]
2003 'High-level telithromycin resistance in laboratory-generated mutants of Streptococcus pneumoniae'
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 [IR Link] [Details]
2003 'The in vitro effects of faropenem on lower respiratory tract pathogens isolated in the United Kingdom'
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 [IR Link] [Details]
2002 'Culturing Chlamydophila pneumoniae'
F. Walsh, J. Willcock, S. G. Amyes. (2002) 'Culturing Chlamydophila pneumoniae'. 14 :312-313 [Details]

Editorial

  Year Publication
2013 The multiple roles of antibiotics and antibiotic resistance in nature.
Walsh, F (2013) The multiple roles of antibiotics and antibiotic resistance in nature. LAUSANNE: Editorial [DOI] [Details]