Article

Ryan, Eimear K. and Clutter, Christy and De Barra, Conor and Jenkins, Benjamin J. and O’Shaughnessy, Simon and Ryan, Odhrán K. and McKenna, Chloe and Heneghan, Helen M. and Walsh, Fiona and Finlay, David K. and Sinclair, Linda V. and Jones, Nicholas and Leung, Daniel T. and O’Shea, Donal and Hogan, Andrew E. (2024) Iron Is Critical for Mucosal-Associated Invariant T Cell Metabolism and Effector Functions. The Journal of Immunology. ISSN 0022-1767

Ryan, Eimear K. and Clutter, Christy and De Barra, Conor and Jenkins, Benjamin J. and O’Shaughnessy, Simon and Ryan, Odhrán K. and McKenna, Chloe and Heneghan, Helen M. and Walsh, Fiona and Finlay, David K. and Sinclair, Linda V. and Jones, Nicholas and Leung, Daniel T. and O’Shea, Donal and Hogan, Andrew E. (2024) Iron Is Critical for Mucosal-Associated Invariant T Cell Metabolism and Effector Functions. The Journal of Immunology, 212 (11). pp. 1706-1713. ISSN 0022-1767

Do, Thi Thuy and Smyth, Cian and Crispie, Fiona and Burgess, Catherine and Brennan, Fiona and Walsh, Fiona (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. p. 159179. ISSN 0048-9697

Tyrrell, Ciara and Do, Thi Thuy and Leigh, Robert J. and Burgess, Catherine M. and Brennan, Fiona P. and Walsh, Fiona (2023) Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland. Science of The Total Environment, 886. p. 163926. ISSN 0048-9697

Corrigan, A. and Leigh, R.J. and Walsh, Fiona and 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 (2). pp. 1-21. ISSN 1056-6171

Leigh, Robert J. and McKenna, Chloe and McWade, Robert and Lynch, Breda and Walsh, Fiona (2022) Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. Journal of Medical Microbiology, 71 (10). ISSN 0022-2615

Leigh, Robert J. and McKenna, Chloe and McWade, Robert and Lynch, Breda and Walsh, Fiona (2022) Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. Journal of Medical Microbiology, 71 (10). pp. 1-27. ISSN 0022-2615

Leigh, Robert J. and Corrigan, Aoife and Murphy, Richard A. and Walsh, Fiona (2022) Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota. Animal Microbiome, 4 (1). ISSN 2524-4671

Margalit, Anatte and Carolan, James C. and Walsh, Fiona (2022) Global protein responses of multidrug resistance plasmid-containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin. Journal of Global Antimicrobial Resistance, 28. pp. 90-96. ISSN 22137165

Margalit, Anatte and Carolan, James C. and Walsh, Fiona (2022) Global protein responses of multidrug resistance plasmid-containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin. Journal of Global Antimicrobial Resistance, 28. pp. 90-96. ISSN 22137165

Do, Thi Thuy and Nolan, Stephen and Hayes, Nicky and O'Flaherty, Vincent and Burgess, Catherine and Brennan, Fiona and Walsh, Fiona (2022) Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion. Environmental Pollution, 305 (119271). pp. 1-11. ISSN 02697491

Smyth, Cian and Leigh, Robert J. and Delaney, Sarah and Murphy, Richard A. and Walsh, Fiona (2022) Shooting hoops: globetrotting plasmids spreading more than just antimicrobial resistance genes across One Health. Microbial Genomics, 8 (000858). pp. 1-10. ISSN 2057-5858

Funk, Tjede and Pharris, Anastasia and Spiteri, Gianfranco and Bundle, Nick and Melidou, Angeliki and Carr, Michael and Gonzalez, Gabriel and Garcia-Leon, Alejandro and Crispie, Fiona and O’Connor, Lois and Murphy, Niamh and Mossong, Joël and Vergison, Anne and Wienecke-Baldacchino, Anke K. and Abdelrahman, Tamir and Riccardo, Flavia and Stefanelli, Paola and Di Martino, Angela and Bella, Antonino and Lo Presti, Alessandra and Casaca, Pedro and Moreno, Joana and Borges, Vítor and Isidro, Joana and Ferreira, Rita and Gomes, João Paulo and Dotsenko, Liidia and Suija, Heleene and Epstein, Jevgenia and Sadikova, Olga and Sepp, Hanna and Ikonen, Niina and Savolainen-Kopra, Carita and Blomqvist, Soile and Möttönen, Teemu and Helve, Otto and Gomes-Dias, Joana and Adlhoch, Cornelia and Walsh, Fiona (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). ISSN 1560-7917

Delaney, Sarah and Do, Thi Thuy and Corrigan, Aoife and Murphy, Richard and Walsh, Fiona (2021) Investigation into the effect of mannan-rich fraction supplementation on the metagenome of broiler chickens. Microbial Genomics, 7 (7). pp. 1-12. ISSN 2057-5858

Gekenidis, Maria-Theresia and Walsh, Fiona and Drissner, David (2021) Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference? Antibiotics, 10 (9). p. 1100. ISSN 2079-6382

Anjum, Muna F and Schmitt, Heike and Börjesson, Stefan and Berendonk, Thomas U and Donner, Erica and Stehling, Eliana Guedes and Boerlin, Patrick and Topp, Edward and Jardine, Claire and Li, Xuewen and Li, Bing and Dolejska, Monika and Madec, Jean-Yves and Dagot, Christophe and Guenther, Sebastian and Walsh, Fiona and Villa, Laura and Veldman, Kees and Sunde, Marianne and Krzeminski, Pawel and Wasyl, Dariusz and Popowska, Magdalena and Järhult, Josef and Örn, Stefan and Mahjoub, Olfa and Mansour, Wejdene and Thái, Đinh Nho and Elving, Josefine and Pedersen, Karl (2021) The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment. Current Opinion in Microbiology, 64. pp. 152-158. ISSN 1369-5274

Rodriguez-Mozaz, Sara and Vaz-Moreira, Ivone and Varela Della Giustina, Saulo and Llorca, Marta and Barceló, Damià and Schubert, Sara and Berendonk, Thomas U. and Michael-Kordatou, Irene and Fatta-Kassinos, Despo and Luis Martinez, Jose and Elpers, Christian and Henriques, Isabel and Jaeger, Thomas and Schwartz, Thomas and Paulshus, Erik and O'Sullivan, Kristin and Pärnänen, Katariina M. M. and Virta, Marko and Do, Thi Thuy and Walsh, Fiona and Manaia, Célia M. (2020) Antibiotic residues in final effluents of European wastewater treatment plants and their impact on the aquatic environment. Environment International, 140 (105733). pp. 1-11. ISSN 0160-4120

Smyth, Cian and O’Flaherty, Aidan and Walsh, Fiona and Do, Thi Thuy (2020) Antibiotic resistant and extended-spectrum β-lactamase producing faecal coliforms in wastewater treatment plant effluent. Environmental Pollution, 262. p. 114244. ISSN 02697491

Purchase, Diane and Abbasi, Golnoush and Bisschop, Lieselot and Chatterjee, Debashish and Ekberg, Christian and Ermolin, Mikhail and Fedotov, Petr and Garelick, Hemda and Isimekhai, Khadijah and Kandile, Nadia G. and Lundström, Mari and Matharu, Avtar and Miller, Bradley W. and Pineda, Antonio and Popoola, Oluseun E. and Retegan, Teodora and Ruedel, Heinz and Serpe, Angela and Sheva, Yehuda and Surati, Kiran R. and Walsh, Fiona and Wilson, Benjamin P. and Wong, Ming Hung (2020) Global occurrence, chemical properties, and ecological impacts of e-wastes (IUPAC Technical Report). Pure and Applied Chemistry, 92 (11). pp. 1733-1767. ISSN 0033-4545

Gekenidis, Maria-Theresia and Rigotti, Serena and Hummerjohann, Jorg and Walsh, Fiona and Drissner, David (2020) Long-Term Persistence of blaCTX-M-15 in Soil and Lettuce after Introducing Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli via Manure or Water. Microorganisms, 8 (11). pp. 1-18. ISSN 2076-2607

Eissenberger, Kristina and Drissner, David and Walsh, Fiona and Weiss, Agnes and Schmidt, Herbert (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. p. 103316. ISSN 07400020

Thuy Do, Thi and Delaney, Sarah and Walsh, Fiona (2019) 16S rRNA gene based bacterial community structure of wastewater treatment plant effluents. FEMS Microbiology Letters, 366. ISSN 0378-1097

Pärnänen, Katariina M. M. and Narciso-da-Rocha, Carlos and Kneis, David and Berendonk, Thomas U. and Cacace, Damlano and Do, Thi Thuy and Elpers, Christian and Fatta-Kassinos, Despo and Henriques, Isabel and Jaeger, Thomas and Karkman, Antti and Martinez, Jose Luis and Michael, Stella G. and Michael-Kordatou, Irene and O’Sullivan, Kristin and Rodriguez-Mozaz, Sara and Schwartz, Thomas and Sheng, Hongjie and Sørum, Henning and Stedtfeld, Robert D. and Tiedje, James M. and Varela Della Giustina, Saulo and Walsh, Fiona and Vaz-Moreira, Ivone and Virta, Marko and Manaia, Célia M. (2019) Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science Advances, 5 (3). ISSN 2375-2548

Pärnänen, Katariina M. M. and Narciso-da-Rocha, Carlos and Kneis, David and Berendonk, Thomas U. and Cacace, Damlano and Thuy Do, Thi and Elpers, Christian and Fatta-Kassinos, Despo and Henriques, Isabel and Jaeger, Thomas and Karkman, Antti and Martinez, Jose Luis and Michael, Stella G and Michael-Kordatou, Irene and O'Sullivan, Kristin and Rodriguez-Mozaz, Sara and Schwartz, Thomas and Sheng, Hongjie and Sørum, Henning and Stedtfeld, Robert D. and Tiedje, James M. and Giustina, Saulo Varela Della and Walsh, Fiona and Vaz-Moreira, Ivone and Virta, Marko and Manaia, Célia M. (2019) Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science Advances, 5 (3). ISSN 2375-2548

Joyce, Aoife and McCarthy, Charley G.P. and Murphy, Sinead and Walsh, Fiona (2019) Antibiotic resistomes of healthy pig faecal metagenomes. Microbial Genomics, 5 (5). ISSN 2057-5858

Karkman, Antti and Do, Thi Thuy and Walsh, Fiona and Virta, Marko P.J. (2018) Antibiotic-Resistance Genes in Waste Water. Trends in Microbiology, 26 (3). pp. 220-228. ISSN 0966-842X

Do, Thi Thuy and Tamames, Javier and Stedtfeld, Robert D. and Guo, Xueping and Murphy, Sinead and Tiedje, James M. and Walsh, Fiona (2018) Antibiotic Resistance Gene Detection in the Microbiome Context. Microbial Drug Resistance, 24 (5). pp. 542-546. ISSN 1076-6294

Gekenidis, Maria-Theresia and Qi, Weihong and Hummerjohann, Jorg and Zbinden, Reinhard and Walsh, Fiona and Drissner, David (2018) Antibiotic-resistant indicator bacteria in irrigation water: High prevalence of extendedspectrum beta-lactamase (ESBL)-producing Escherichia coli. PLoS ONE, 13 (11). ISSN 1932-6203

Walsh, Fiona (2018) Antimicrobial resistance and one health. Microbiology Today Magazine, Feb.

Delaney, Sarah and Murphy, Richard and Walsh, Fiona (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 (1731). ISSN 1664-302X

Gekenidis, Maria-Theresia and Schöner, Ulrich and von Ah, Ueli and Schmelcher, Mathias and Walsh, Fiona and Drissner, D. (2018) Tracing back multidrug-resistant bacteria in fresh herb production: from chive to source through the irrigation water chain. FEMS Microbiology Ecology, 94 (11). fiy149. ISSN 1574-6941

Weiss, A. and Scheller, F. and Oggenfuss, M. and Walsh, Fiona and Frey, Jurg E. and Drissner, D. and Schmidt, H. (2016) Analysis of the bacterial epiphytic microbiota of oak leaf lettuce with 16S ribosomal RNA gene analysis. Journal of Microbiology, Biotechnology and Food Sciences, 5 (3). pp. 271-276. ISSN 1338-5178

Fitzpatrick, David A. and Walsh, Fiona (2016) Antibiotic resistance genes across a wide variety of metagenomes. FEMS Microbiology Ecology, 92 (2). fiv168. ISSN 1574-6941

Thanner, Sophie and Drissner, D. and Walsh, Fiona (2016) Antimicrobial Resistance in Agriculture. mBio, 7 (2). e02227-15. ISSN 2150-7511

Fouhy, Fiona and Stanton, Catherine and Cotter, Paul D. and Hill, Colin and Walsh, Fiona (2015) Proteomics as the final step in the functional metagenomics study of antimicrobial resistance. Frontiers in Microbiology, 6 (172). pp. 1-6. ISSN 1664-302X

Berendonk, Thomas U. and Manaia, Célia M. and Merlin, Christophe and Fatta‑Kassinos, Despo and Cytryn, Eddie and Walsh, Fiona and Bürgmann, Helmut and Sørum, Henning and Norström, Madelaine and Pon, Marie-Noëlle and Kreuzinger, Norbert and Huovinen, Pentti and Stefani, Stefania and Schwartz, Thomas and Kisand, Veljo and Baquero, Fernando and Martinez, Jose Luis (2015) Tackling antibiotic resistance: the environmental framework. Nature Reviews Microbiology, 13. pp. 310-317. ISSN 1740-1534

Dunbar, John P. and Zarelli, Micaela and Martin, Stephen A. and Gandola, Robert and Kavanagh, Kevin and Walsh, Fiona and Rivas, Jesus A. (2015) Trunk vertebrae osteomyelitis in a spectacled caiman (Caiman crocodilus). Herpetological Bulletin, 134. pp. 15-18. ISSN 1473-0928

Walsh, Fiona and Pelludat, C. and Duffy, B. and Smith, D.P. and Owens, Sarah M. and Frey, Jurg E. and Holliger, E. (2014) Einfluss von Streptomycin in Apfelanlagen auf Antibiotika-Resistenzen in der Umwelt. Agrarforschung Schweiz 5(7+08), 300-305, 2014, 5 (7-8). pp. 300-305.

Bunge, John and Willis, Amy and Walsh, Fiona (2014) Estimating the Number of Species in Microbial Diversity Studies. The Annual Review of Statistics and its Applications, 1. pp. 427-445.

Walsh, Fiona and Smith, Daniel P. and Owens, Sarah M. and Duffy, Brion and Frey, Jurg E. (2014) Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities. Frontiers in Microbiology. ISSN 1664-302X

Duffy, Brion and Holliger, E. and Walsh, Fiona (2014) Streptomycin use in apple orchards did not increase abundance of mobile resistance genes. FEMS Microbiology Letters, 350. pp. 180-189. ISSN 0378-1097

Walsh, Fiona and Duffy, Brion (2013) The Culturable Soil Antibiotic Resistome: A Community of Multi-Drug Resistant Bacteria. PLoS ONE. ISSN 1932-6203

Walsh, Fiona and Amyes, Sebastian G.B. and Duffy, Brian (2013) Challenging the concept of bacteria subsisting on antibiotics. International Journal of Antimicrobial Agents, 41. pp. 558-563. ISSN 0924-8579

Walsh, Fiona (2013) Investigating antibiotic resistance in non-clinical environments. Frontiers in Microbiology. ISSN 1664-302X

Cantas, L. and Shah, Syed Q.A. and Cavaco, L.M. and Manaia, Célia M. and Walsh, Fiona and Popowska, Magdalena and Garelick, H. and Bürgmann, H. and Sørum, Henning (2013) A brief multi-disciplinary review on antimicrobial resistance in medicine and its linkage to the global environmental microbiota. Frontiers in Microbiology, 4 (96). ISSN 1664-302X

Walsh, Fiona and Rogers, Thomas R. (2012) Comparison of plasmid-mediated quinolone resistance and extended-spectrum b-lactamases in third-generation cephalosporin-resistant Enterobacteriaceae from four Irish hospitals. Journal of Medical Microbiology, 61. pp. 142-147. ISSN 0022-2615

Popowska, Magdalena and Rzeczycka, Marzenna and Miernik, Antoni and Krawczyk-Balska, Agata and Walsh, Fiona and Duffy, Brion (2012) Influence of Soil Use on Prevalence of Tetracycline, Streptomycin, and Erythromycin Resistance and Associated Resistance Genes. Antimicrobial Agents and Chemotherapy, 56 (3). pp. 1434-1443. ISSN 0066-4804

Walsh, Fiona and Ingenfeld, A. and Zampicolli, M. and Hilber-Bodmer, M. and Frey, Jurg E. and Duffy, B. (2011) Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems. Journal of Microbiological Methods, 86 (2). pp. 150-155. ISSN 0167-7012

Walsh, Fiona and Cooke, Niamh M. and Smith, Stephen G. and Moran, Gary P. and Cooke, Fiona J. and Ivens, Alasdair and Wain, John and Rogers, Thomas R. (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 (6). pp. 593-598. ISSN 0924-8579

Boo, T.W. and Walsh, Fiona and Crowley, B. (2009) Molecular characterization of carbapenem-resistant Acinetobacter species in an Irish university hospital: predominance of Acinetobacter genomic species 3. Journal of Medical Microbiology, 58 (2). pp. 209-216. ISSN 0022-2615

Roche, C. and Boo, T.W. and Walsh, Fiona and Crowley, B. (2008) Detection and molecular characterisation of plasmidic AmpC b-lactamases in Klebsiella pneumoniae isolates from a tertiary-care hospital in Dublin, Ireland. Clinical Microbiology and Infection, 14 (6). pp. 616-618. ISSN 1198-743X

Walsh, Fiona and Rogers, Thomas R. (2008) Detection of blaVIM-2 carbapenemase in Pseudomonas aeruginosa in Ireland. Journal of Antimicrobial Chemotherapy, 61 (1). pp. 219-220. ISSN 0305-7453

Amyes, Sebastian G.B. and Walsh, Fiona and Bradley, John S. (2007) Best in class: a good principle for antibiotic usage to limit resistance development? Journal of Antimicrobial Chemotherapy, 59. pp. 825-826. ISSN 0305-7453

Walsh, Fiona (2007) Doripenem: A new carbapenem antibiotic a review of comparative antimicrobial and bactericidal activities. Therapeutics and Clinical Risk Management, 3 (5). pp. 789-794. ISSN 1176-6336

Walsh, Fiona and Bracher, S. and Turner, P. and Amyes, Sebastian G.B. (2007) Preferential Selection of IMP and VIM Metallo-β-Lactamases by Imipenem in Pseudomonas aeruginosa. Experimental Chemotherapy, 53. pp. 407-409. ISSN 0536–0407

Boo, T.W. and Walsh, Fiona and Crowley, B. (2006) First report of OXA-23 carbapenemase in clinical isolates of Acinetobacter species in the Irish Republic. Journal of Antimicrobial Chemotherapy, 58 (5). pp. 1101-1102. ISSN 0305-7453

Walsh, Fiona and Bracher, S. and Turner, P. and Amyes, Sebastian G.B. (2005) Epidemiological analysis of carbapenem-sensitive and -resistant Pseudomonas aeruginosa. Journal of Hospital Infection, 60 (3). pp. 240-244. ISSN 0195-6701

Walsh, Fiona and Carnegy, Francis and Willcock, Joanne and Amyes, Sebastian G.B. (2004) Comparative in vitro activity of telithromycin against macrolide-resistant and -susceptible Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae. Journal of Antimicrobial Chemotherapy, 53 (5). pp. 793-796. ISSN 0305-7453

Walsh, Fiona and Amyes, Sebastian G.B. (2004) Microbiology and drug resistance mechanisms of fully resistant pathogens. Current Opinion in Microbiology, 7. pp. 439-444. ISSN 1369-5274

Walsh, Fiona and Willcock, Joanne and Amyes, Sebastian G.B. (2003) High-level telithromycin resistance in laboratory-generated mutants of Streptococcus pneumoniae. Journal of Antimicrobial Chemotherapy, 52 (3). pp. 345-353. ISSN 0305-7453

Walsh, Fiona and Amyes, A.K.B. and Amyes, Sebastian G.B. (2003) The in vitro effects of faropenem on lower respiratory tract pathogens isolated in the United Kingdom. International Journal of Antimicrobial Agents, 21 (2). pp. 581-584. ISSN 0924-8579

Walsh, Fiona and Willcock, Joanne and Amyes, Sebastian G.B. (2002) Culturing Chlamydophila pneumoniae. Journal of Chemotherapy, 14 (3). pp. 312-313. ISSN 1120-009X