Biography
I have over 10 years of experience working in the Higher Education & Healthcare sector in the UK and Ireland as a Research Assistant, Postdoctoral Research Fellow & Molecular Epidemiologist.
Following graduating from NUI Maynooth in 2008 with a B.Sc. in Biological Sciences, I was offered a Research Assistant position at The University of Oxford, Nuffield Dept. of Clinical & Experimental Medicine. Here I spent 2 years working as part of a multidisciplinary team on the SPARTAC trial. I was responsible for longitudinal sequencing of samples from patients acutely infected with HIV.
In 2011, I secured a place to complete a Masters in Virology at Imperial College London and shortly later, I successfully secured a place to complete a Ph.D. in Molecular Microbiology of the fungal pathogen Candida albicans at the Dublin Dental University Hospital, Trinity College Dublin. I was later appointed to Postdoctoral Fellow, pioneering the implementation of 3rd generation sequencing in the Molecular Microbiology group. In addition to my research responsibilities, I was responsible for coordinating and disseminating the Problem Based Learning course content as tutor for Dental Science students. Furthermore, I oversaw undergraduates carrying out research projects as part of the Microbiology course at Trinity and have demonstrated and lectured on the following courses within Trinity College; BY1101 Molecular & Cellular Biology, BY2202 Vertebrate Form & Function, BY2205 Microbiology and BY2209 Immunity & Infection. In addition to this, I lecture on the MSc Healthcare Infection course.
In 2019 I took up a position as a Clinical Scientist at the Irish Mycobacterium Reference Laboratory were I was primarily tasked with helping with the development of Whole Genome Sequencing, in conjunction with the National MRSA Reference Laboratory, as part of routine analysis and outbreak investigation. This was a vast undertaking of working in conjunction with IT and MS Azure to develop a robust IT infrastructure.
As of 2023, I am based in The Public Health Laboratory at Cherry Orchard Hospital where I mange three National Reference Laboratory services (C. difficile, VTEC and Campylobacter). This involves developing the sequencing capabilities of the laboratory to perform relatedness analysis of community onset and hospital outbreaks. I work in conjunction with Public Health Areas within Ireland and the EU for local and cross board outbreaks.
Publications and Further Research Outputs
Peer-Reviewed Publications
Dolan A.-M., Hoban T., Brennan G., Flanagan P.R., O'Rourke S., Teoh T.K., Boyle B., Mellerick L., Toolan S., Flynn C., Wagener J., O'Connell B., Magnusiomyces capitatus, an Unusual Cause of Invasive Fungal Infections in Neutropenic Patients: Case Reports and Outbreak Investigation, Mycopathologia, 190, (1), 2025
Diana Espadinha, Emma Roycroft, Peter R. Flanagan, Simone Mok, Eleanor McNamara, Thomas R. Rogers, Margaret M. Fitzgibbon, Validation and implementation of whole-genome sequencing-based analytical methods for molecular surveillance and relatedness analysis of Mycobacterium tuberculosis complex isolates at a national reference laboratory, Heliyon, 10, (22), 2024, pe40279
Mok S, Roycroft E, Flanagan PR, Wagener J, Fitzgibbon MM., Investigation of genomic mutations and their association with phenotypic resistance to new and repurposed drugs in Mycobacterium tuberculosis complex clinical isolates., The Journal of antimicrobial chemotherapy, 2023, pdkad252
Fletcher J, O'Connor-Moneley J, Frawley D, Flanagan PR, Alaalm L, Menendez-Manjon P, Estevez SV, Hendricks S, Woodruff AL, Buscaino A, Anderson MZ, Sullivan DJ, Moran GP., Deletion of the Candida albicans TLO gene family using CRISPR-Cas9 mutagenesis allows characterisation of functional differences in " - ß- and "- TLO gene function., PLoS genetics, 19, (12), 2023, pe1011082
Qi W, Acosta-Zaldivar M, Flanagan PR, Liu NN, Jani N, Fierro JF, Andrés MT, Moran GP, Köhler JR., Stress- and metabolic responses of Candida albicans require Tor1 kinase N-terminal HEAT repeats., PLoS pathogens, 18, (6), 2022, pe1010089
Simone Mok, Peter R. Flanagan, Emma Roycroft, Thomas R. Rogers, Margaret M. Fitzgibbon, Julie C. Dunning Hotopp, Draft Genome Sequences of Clinical Respiratory Isolates of Mycobacterium goodii Recovered in Ireland, Microbiology Resource Announcements, 10, (31), 2021
Roycroft E, Fitzgibbon MM, Kelly DM, Scully M, McLaughlin AM, Flanagan PR, Gordon SV, Rogers TR, Keane J, O Meara M, The largest prison outbreak of TB in Western Europe investigated using whole-genome sequencing., The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 2021
Fitzgibbon MM, Roycroft E, Sheehan G, Mc Laughlin AM, Quintyne KI, Brabazon E, O'Meara M, Flanagan PR, Seagar AL, Laurenson IF, Keane J, Rogers TR., False detection of rifampicin resistance using Xpert® MTB/RIF Ultra assay due to an A451V mutation in Mycobacterium tuberculosis., JAC Antimicrob Resist, 3, (3), 2021, pdlab101
Redondo N, Mok S, Montgomery L, Flanagan PR, McNamara E, Smyth EG, O'Sullivan N, Schaffer K, Rogers TR, Fitzgibbon MM, Genomic Analysis of Mycobacterium abscessus Complex Isolates Collected in Ireland between 2006 and 2017., Journal of clinical microbiology, 2020
McManus BA, O'Connor AM, Egan SA, Flanagan PR, Coleman DC., First description of arginine catabolic mobile element (ACME) type VI harboring the kdp operon only in Staphylococcus epidermidis using short and long read whole genome sequencing: Further evidence of ACME diversity., Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 71, 2019, p51-53
Peter R. Flanagan, Jessica Fletcher, Hannah Boyle, Razvan Sulea, Gary P. Moran, Derek J. Sullivan, Expansion of the TLO gene family enhances the virulence of Candida species, PLoS One, 13, (7), 2018
Liu NN, Flanagan PR, Zeng J, Jani NM, Cardenas ME, Moran GP, Köhler JR., Phosphate is the third nutrient monitored by TOR in Candida albicans and provides a target for fungal-specific indirect TOR inhibition., Proceedings of the National Academy of Sciences of the United States of America, 114, (24), 2017, p6346-6351
Flanagan PR, Liu NN, Fitzpatrick DJ, Hokamp K, Köhler JR, Moran GP., The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation., mSphere, 2, (6), 2017
Roberts, Hannah E and Hurst, Jacob and Robinson, Nicola and Brown, Helen and Flanagan, Peter and Vass, Laura and Fidler, Sarah and Weber, Jonathan and Babiker, Abdel and Phillips, Rodney E and McLean, Angela R and Frater, John and SPARTAC Trial Investigators, Structured Observations Reveal Slow HIV-1 CTL Escape, PLoS Genetics, 11, (2), 2015, pe1004914
Yager, Nicole and Robinson, Nicola and Brown, Helen and Flanagan, Peter and Frater, John and Fidler, Sarah and Weber, Jonathan and Phillips, Rodney and {SPARTAC Trial Investigators, Longitudinal analysis of an HLA-B*51-restricted epitope in integrase reveals immune escape in early HIV-1 infection., AIDS (London, England), 27, (3), 2013, p313--323
English, Suzanne and Katzourakis, Aris and Bonsall, David and Flanagan, Peter and Duda, Anna and Fidler, Sarah and Weber, Jonathan and McClure, Myra and {SPARTAC Trial Investigators, Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants., Retrovirology, 8, (1), 2011, p54
Barnes, Eleanor and Flanagan, Peter and Brown, Anthony and Robinson, Nicola and Brown, Helen and McClure, Myra and Oxenius, Annette and Collier, Jane and Weber, Jonathan and G{\"u, Failure to detect xenotropic murine leukemia virus-related virus in blood of individuals at high risk of blood-borne viral infections., The Journal of infectious diseases, 202, (10), 2010, p1482--1485