Publications and Further Research Outputs
Peer-Reviewed Publications
Addington E, Wale KR, Horsburgh E, Fargeas M, Spathis L, Le"niak W, Flavin S, Rimbi PT, Mark DR, Sandalli S, Serrano E, Blackburn G, Regnault C, Whitfield PD, Connolly JPR, Roe AJ, O'Boyle N., Catabolism of serine enantiomers represses enterohemorrhagic Escherichia coli virulence factors via modulation of the nitrogen stress response., Proceedings of the National Academy of Sciences of the United States of America, 123, (12), 2026, pe2532916123
Ella Rellis, Nicky O'Boyle, The glucose uptake inhibitor SgrS is induced by D-serine yet does not contribute to growth arrest in enterohaemorrhagic Escherichia coli, Microbiology, 171, (1), 2026, p001648
DR Mark, N O'Boyle, KR Wale, SK Tucker, RE McHugh, AJ Roe, Aurodox inhibits type III secretion in multiple Gram-negative pathogens, Open Biology, 14, (11), 2024, p240240
Rimbi PT, O'Boyle N, Douce GR, Pizza M, Rosini R, Roe AJ., Enhancing a multi-purpose artificial urine for culture and gene expression studies of uropathogenic Escherichia coli strains., Journal of applied microbiology, 135, (4), 2024, plxae067
Kabo R Wale, Nicky O'Boyle, Rebecca McHugh, Ester Serrano, David Mark, Gillian R Douce, James PR Connolly, Andrew J Roe, A master regulator of central carbon metabolism directly activates virulence gene expression in attaching and effacing pathogens, PLoS Pathogens, 20, (10), 2024, pe1012451
Connolly JPR, Turner NCA, Hallam JC, Rimbi PT, Flett T, McCormack MJ, Roe AJ, O'Boyle N, Transcriptional response to D-serine stress in distinct E. coli pathotypes, 1, MORF Open Science, 2024
Hallam JC, Sandalli S, Floria I, Turner NCA, Tang-Fichaux M, Oswald E, O'Boyle N, Roe AJ., D-Serine reduces the expression of the cytopathic genotoxin colibactin., Microbial cell (Graz, Austria), 10, (3), 2023, p63-77
O'Boyle N, Douce GR, Farrell G, Rattray NJW, Schembri MA, Roe AJ, Connolly JPR., Distinct ecological fitness factors coordinated by a conserved Escherichia coli regulator during systemic bloodstream infection., Proceedings of the National Academy of Sciences of the United States of America, 120, (1), 2023, pe2212175120
Nicky O'Boyle, Aoife Boyd, Validation of a random Vibrio parahaemolyticus genomic library by selection of quinolone resistance in a heterologous host, Microbiology, 168, (5), 2022
Connolly JPR, Turner NCA, Serrano E, Rimbi PT, Browning DF, O'Boyle N, Roe AJ., Control of resistance against bacteriophage killing by a metabolic regulator in meningitis-associated Escherichia coli., Proceedings of the National Academy of Sciences of the United States of America, 119, (45), 2022, pe2210299119
Mordue J, O'Boyle N, Gadegaard N, Roe AJ., The force awakens: The dark side of mechanosensing in bacterial pathogens., Cellular signalling, 78, 2021, p109867
Connolly JPR, Turner NCA, Hallam JC, Rimbi PT, Flett T, McCormack MJ, Roe AJ, O'Boyle N, d-Serine induces distinct transcriptomes in diverse Escherichia coli pathotypes., Microbiology (Reading, England), 2021
Connolly JPR, Turner NCA, Hallam JC, Rimbi PT, Flett T, McCormack MJ, Roe AJ, O'Boyle N, D-serine induces distinct transcriptomes in diverse Escherichia coli pathotypes., Microbiology, 167, (10), 2021, p001093
O'Boyle N, Roe AJ., Heterogeneity in populations of enterohaemorrhagic Escherichia coli undergoing D-serine adaptation., Current genetics, 67, (2), 2021, p221-224
Connolly JPR, Roe AJ, O'Boyle N., Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria., Critical reviews in microbiology, 47, (1), 2021, p126-140
O'Boyle N, Turner NCA, Roe AJ, Connolly JPR., Plastic Circuits: Regulatory Flexibility in Fine Tuning Pathogen Success., Trends in microbiology, 28, (5), 2020, p360-371
O'Boyle N, Berry CC, Davies RL., Differentiated ovine tracheal epithelial cells support the colonisation of pathogenic and non-pathogenic strains of Mannheimia haemolytica., Scientific reports, 10, (1), 2020, p14971
Fox S, Goswami C, Holden M, Connolly JPR, Mordue J, O'Boyle N, Roe A, Connor M, Leanord A, Evans TJ., A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage., Scientific reports, 10, (1), 2020, p4135
Connolly JPR, O'Boyle N, Roe AJ., Widespread Strain-Specific Distinctions in Chromosomal Binding Dynamics of a Highly Conserved Escherichia coli Transcription Factor., mBio : Duplicate, marked for deletion, 11, (3), 2020, pe01058-20
O'Boyle N, Connolly JPR, Tucker NP, Roe AJ., Genomic plasticity of pathogenic Escherichia coli mediates d-serine tolerance via multiple adaptive mechanisms., Proceedings of the National Academy of Sciences of the United States of America, 117, (36), 2020, p22484-22493
McHugh RE, O'Boyle N, Connolly JPR, Hoskisson PA, Roe AJ., Characterization of the Mode of Action of Aurodox, a Type III Secretion System Inhibitor from Streptomyces goldiniensis., Infection and immunity, 87, (2), 2019, pe00595-18
Connolly JPR, O'Boyle N, Turner NCA, Browning DF, Roe AJ., Distinct intraspecies virulence mechanisms regulated by a conserved transcription factor., Proceedings of the National Academy of Sciences of the United States of America, 116, (39), 2019, p19695-19704
O'Boyle N, Connolly JPR, & Roe AJ, Tracking elusive cargo: Illuminating spatio"temporal Type 3 effector protein dynamics using reporters., Cellular Microbiology, 20, (1), 2018, pe12797
Connolly JP, Slater SL, O"Boyle N, Goldstone RJ, Crepin VF, Ruano-Gallego D, Herzyk P, Smith DG, Douce GR, Frankel G, Roe AJ, Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion., Nature Communications., 9, (1), 2018, p4187
O'Boyle N, Sutherland E, Berry CC, & Davies RL, Optimisation of growth conditions for ovine airway epithelial cell differentiation at an air-liquid interface., Plos one, 13, (3), 2018, pe0193998
O'Boyle N, Sutherland E, Berry CC, & Davies RL, Temporal dynamics of ovine airway epithelial cell differentiation at an air-liquid interface., PloS one, 12, (7), 2017, pe0181583
O'Boyle N, Boyd A., Manipulation of intestinal epithelial cell function by the cell contact-dependent type III secretion systems of Vibrio parahaemolyticus., Frontiers in cellular and infection microbiology, 3, 2014, p114
O'Boyle N, Houeix B, Kilcoyne M, Joshi L, Boyd A., The MSHA pilus of Vibrio parahaemolyticus has lectin functionality and enables TTSS-mediated pathogenicity., International journal of medical microbiology : IJMM, 303, (8), 2013, p563-573
Research Expertise
Projects
- Title
- Targeting opportunistic Enterobacteriaceae in ileal Crohn's disease using D-amino acids
- Summary
- Inflammatory bowel disease (IBD) comprises distinct clinical subtypes, with unique microbial associations, pathological features and responses to treatment. Ileal Crohn's disease (ICD) has the strongest association with over-proliferation of a specific family of bacteria, the Enterobacteriaceae. While their role in disease progression is poorly understood, they are considered an attractive target for therapies aimed at dampening IBD-associated inflammation. I will investigate the prevalence of tissue-invasive Enterobacteriaceae in a cohort of Irish patients and explore the potential of D-amino acids (DAAs) to inhibit virulence and proliferation of these bacteria using in vitro enteroid models. DAAs are garnering increasing interest for their ability to modulate the behaviour of pathogenic bacteria. Several DAAs were recently shown to be depleted in patients with ulcerative colitis and could reduce Enterobacteriaceae blooms, and inflammation in mouse models of colitis. Enterobacteriaceae burden in patient biopsies will be assessed by isolation on bacterial growth media, PCR strain profiling, shotgun metagenomics and histology. I will investigate whether ICD-associated bacterial taxa correlate with altered faecal DAA profiles, comparing our cohort of patients with ten healthy controls by chiral mass spectrometry. To assess toxicity, and efficacy in inhibiting the proliferation of Enterobacteriaceae in a model more reflective of human physiology, I will culture enteroids from this cohort and study the effect of DAAs on infection with Enterobacteriaceae. Importantly, DAAs are prevalent in many foods, particularly fermented foods. My team will include an IBD patient group to design a food questionnaire exploring how fermented foods modulate IBD symptoms and to identify other foods that trigger flare ups in symptoms. We will then profile the DAA content of these foodstuffs. The outcome of this study will be an enhanced understanding of the role of Enterobacteriaceae in ICD and a pre-clinical assessment of the suitability of DAAs as IBD biomarkers and therapeutics.
- Funding Agency
- Health Research Board
- Date From
- 01/09/2025
- Date To
- 31/08/2029
- Title
- Treasures of the Deep: Bioprospecting Marine Sponge Streptomyces for Novel Anti-Virulence Therapeutics
- Funding Agency
- Trinity College Dublin
- Date From
- 01/09/2025
- Date To
- 31/08/2029
- Title
- Deciphering Blue Ecosystem Chemical Communication Networks for Sustainable Next Generation solutions to the Antimicrobial Resistance Crisis.
- Funding Agency
- Irish Research Council
- Date From
- 02/09/24
- Date To
- 02/092028
- Title
- Assessing the effect of over the counter analgesic drugs on antimicrobial resistance in diverse pathogenic E. coli
- Summary
- Antimicrobial resistance is a global health crisis, causing over 1.3 million deaths annually and threatening modern medicine. While antibiotic misuse is a known driver of resistance, non-antibiotic analgesic pharmaceuticals including non-steroidal anti-inflammatory drugs may also play a role. Recent studies have shown that common painkillers that are often co-administered with antimicrobials can inhibit growth and induce bacterial stress responses, potentially enhancing the selection of resistance. Crucially however, these studies have only used lab-adapted strains such as E. coli K-12, not real-world pathogens. Here, we will investigate the response of E. coli pathotypes associated with urinary tract infection, bloodstream infection, neonatal meningitis, and inflammatory bowel disease to various combinations of antimicrobials and non-steroidal anti-inflammatory drugs. Four clinically used antimicrobials with different cellular targets (Trimethoprim/sulfamethoxazole (TMP-SMX), ciprofloxacin, ampicillin and nitrofurantoin) will be tested in combination with acetaminophen, ibuprofen, naproxen, and aspirin. Minimum inhibitory concentration (MIC) assays will be carried out to determine gross alterations in resistance profiles. Growth curves will be constructed at " MIC concentrations to examine whether stress induced by analgesic drugs compounds the effect of antimicrobials. Efficiency of bacterial killing will be determined in the presence and absence of analgesic drugs by plating following various periods of incubation. Finally, the effect of analgesic drugs on the resistance evolution will be determined using a lab-based evolution study. The insight gained from these experiments will help inform appropriate usage of pain relieving medications for bacterial infections while minimising the selection of resistance.
- Funding Agency
- Health Research Board
- Date From
- 01/06/26
- Date To
- 31/07/26
- Title
- D-serine: A dietary solution to enteric infection or a potentiator of pathogen evolution?
- Funding Agency
- Tenovus Scotland
- Date From
- 01/11/2019
Recognition
Awards and Honours
SEFS New Connections Summer Research Bursary (University College, Cork)
SEFS New Connections Grant (University College, Cork)
Tenovus Scotland Pilot Grant (Tenovus Scotland)
Professor L. Kieran Dunican Memorial Medal (NUI, Glaway)
Federation of European Biochemical Societies Youth Travel Fund (YTF) Fellowship
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Microbiology Society Travel/Conference Grant
Memberships
Irish Division of the Microbiology Society
Microbiology Society