Article

Ryan, Eimear K., Clutter, Christy, De Barra, Conor, Jenkins, Benjamin J., O’Shaughnessy, Simon, Ryan, Odhrán K., McKenna, Chloe, Heneghan, Helen M., Walsh, Fiona, Finlay, David K., Sinclair, Linda V., Jones, Nicholas, Leung, Daniel T., 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., Clutter, Christy, De Barra, Conor, Jenkins, Benjamin J., O’Shaughnessy, Simon, Ryan, Odhrán K., McKenna, Chloe, Heneghan, Helen M., Walsh, Fiona, Finlay, David K., Sinclair, Linda V., Jones, Nicholas, Leung, Daniel T., 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, Smyth, Cian, Crispie, Fiona, Burgess, Catherine, 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, Do, Thi Thuy, Leigh, Robert J., Burgess, Catherine M., 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., Leigh, R.J., 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., McKenna, Chloe, McWade, Robert, 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., McKenna, Chloe, McWade, Robert, 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., Corrigan, Aoife, 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, 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, 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, Nolan, Stephen, Hayes, Nicky, O'Flaherty, Vincent, Burgess, Catherine, 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, Leigh, Robert J., Delaney, Sarah, 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, Pharris, Anastasia, Spiteri, Gianfranco, Bundle, Nick, Melidou, Angeliki, Carr, Michael, Gonzalez, Gabriel, Garcia-Leon, Alejandro, Crispie, Fiona, O’Connor, Lois, Murphy, Niamh, Mossong, Joël, Vergison, Anne, Wienecke-Baldacchino, Anke K., Abdelrahman, Tamir, Riccardo, Flavia, Stefanelli, Paola, Di Martino, Angela, Bella, Antonino, Lo Presti, Alessandra, Casaca, Pedro, Moreno, Joana, Borges, Vítor, Isidro, Joana, Ferreira, Rita, Gomes, João Paulo, Dotsenko, Liidia, Suija, Heleene, Epstein, Jevgenia, Sadikova, Olga, Sepp, Hanna, Ikonen, Niina, Savolainen-Kopra, Carita, Blomqvist, Soile, Möttönen, Teemu, Helve, Otto, Gomes-Dias, Joana, 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, Do, Thi Thuy, Corrigan, Aoife, 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, 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, Schmitt, Heike, Börjesson, Stefan, Berendonk, Thomas U, Donner, Erica, Stehling, Eliana Guedes, Boerlin, Patrick, Topp, Edward, Jardine, Claire, Li, Xuewen, Li, Bing, Dolejska, Monika, Madec, Jean-Yves, Dagot, Christophe, Guenther, Sebastian, Walsh, Fiona, Villa, Laura, Veldman, Kees, Sunde, Marianne, Krzeminski, Pawel, Wasyl, Dariusz, Popowska, Magdalena, Järhult, Josef, Örn, Stefan, Mahjoub, Olfa, Mansour, Wejdene, Thái, Đinh Nho, 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, Vaz-Moreira, Ivone, Varela Della Giustina, Saulo, Llorca, Marta, Barceló, Damià, Schubert, Sara, Berendonk, Thomas U., Michael-Kordatou, Irene, Fatta-Kassinos, Despo, Luis Martinez, Jose, Elpers, Christian, Henriques, Isabel, Jaeger, Thomas, Schwartz, Thomas, Paulshus, Erik, O'Sullivan, Kristin, Pärnänen, Katariina M. M., Virta, Marko, Do, Thi Thuy, 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, O’Flaherty, Aidan, 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, Abbasi, Golnoush, Bisschop, Lieselot, Chatterjee, Debashish, Ekberg, Christian, Ermolin, Mikhail, Fedotov, Petr, Garelick, Hemda, Isimekhai, Khadijah, Kandile, Nadia G., Lundström, Mari, Matharu, Avtar, Miller, Bradley W., Pineda, Antonio, Popoola, Oluseun E., Retegan, Teodora, Ruedel, Heinz, Serpe, Angela, Sheva, Yehuda, Surati, Kiran R., Walsh, Fiona, 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, Rigotti, Serena, Hummerjohann, Jorg, 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, Drissner, David, Walsh, Fiona, 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, 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., Narciso-da-Rocha, Carlos, Kneis, David, Berendonk, Thomas U., Cacace, Damlano, Do, Thi Thuy, Elpers, Christian, Fatta-Kassinos, Despo, Henriques, Isabel, Jaeger, Thomas, Karkman, Antti, Martinez, Jose Luis, Michael, Stella G., Michael-Kordatou, Irene, O’Sullivan, Kristin, Rodriguez-Mozaz, Sara, Schwartz, Thomas, Sheng, Hongjie, Sørum, Henning, Stedtfeld, Robert D., Tiedje, James M., Varela Della Giustina, Saulo, Walsh, Fiona, Vaz-Moreira, Ivone, 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., Narciso-da-Rocha, Carlos, Kneis, David, Berendonk, Thomas U., Cacace, Damlano, Thuy Do, Thi, Elpers, Christian, Fatta-Kassinos, Despo, Henriques, Isabel, Jaeger, Thomas, Karkman, Antti, Martinez, Jose Luis, Michael, Stella G, Michael-Kordatou, Irene, O'Sullivan, Kristin, Rodriguez-Mozaz, Sara, Schwartz, Thomas, Sheng, Hongjie, Sørum, Henning, Stedtfeld, Robert D., Tiedje, James M., Giustina, Saulo Varela Della, Walsh, Fiona, Vaz-Moreira, Ivone, 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, McCarthy, Charley G.P., Murphy, Sinead and Walsh, Fiona (2019) Antibiotic resistomes of healthy pig faecal metagenomes. Microbial Genomics, 5 (5). ISSN 2057-5858

Karkman, Antti, Do, Thi Thuy, 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, Tamames, Javier, Stedtfeld, Robert D., Guo, Xueping, Murphy, Sinead, 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, Qi, Weihong, Hummerjohann, Jorg, Zbinden, Reinhard, 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, 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, Schöner, Ulrich, von Ah, Ueli, Schmelcher, Mathias, 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., Scheller, F., Oggenfuss, M., Walsh, Fiona, Frey, Jurg E., 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, Drissner, D. and Walsh, Fiona (2016) Antimicrobial Resistance in Agriculture. mBio, 7 (2). e02227-15. ISSN 2150-7511

Fouhy, Fiona, Stanton, Catherine, Cotter, Paul D., 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., Manaia, Célia M., Merlin, Christophe, Fatta‑Kassinos, Despo, Cytryn, Eddie, Walsh, Fiona, Bürgmann, Helmut, Sørum, Henning, Norström, Madelaine, Pon, Marie-Noëlle, Kreuzinger, Norbert, Huovinen, Pentti, Stefani, Stefania, Schwartz, Thomas, Kisand, Veljo, 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., Zarelli, Micaela, Martin, Stephen A., Gandola, Robert, Kavanagh, Kevin, 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, Pelludat, C., Duffy, B., Smith, D.P., Owens, Sarah M., 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, 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, Smith, Daniel P., Owens, Sarah M., 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, 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, 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., Shah, Syed Q.A., Cavaco, L.M., Manaia, Célia M., Walsh, Fiona, Popowska, Magdalena, Garelick, H., 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, Rzeczycka, Marzenna, Miernik, Antoni, Krawczyk-Balska, Agata, 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, Ingenfeld, A., Zampicolli, M., Hilber-Bodmer, M., 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, Cooke, Niamh M., Smith, Stephen G., Moran, Gary P., Cooke, Fiona J., Ivens, Alasdair, 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., 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., Boo, T.W., 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., 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, Bracher, S., 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., 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, Bracher, S., 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, Carnegy, Francis, 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, 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, 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, Willcock, Joanne and Amyes, Sebastian G.B. (2002) Culturing Chlamydophila pneumoniae. Journal of Chemotherapy, 14 (3). pp. 312-313. ISSN 1120-009X