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Dr. Peter Flanagan

Visiting Research Fellow (Clinical Microbiology)
      
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Dr. Peter Flanagan

Visiting Research Fellow (Clinical Microbiology)

 peter.r.flanagan@tcd.ie

 


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.
  Biological Sciences   HIV virology and pathogenesis   Long Read Sequencing   MICROBIOLOGY   molecular biology   MOLECULAR-BIOLOGY   Mycobacterium tuberculosis   Oral microbiology   Oxford Nanopore Sequencing   RESISTANT TUBERCULOSIS   Viral Studies (Virology)   Virology   Virology and viral pathogenesis   Whole Genome Sequencing
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English Fluent Fluent Fluent
Irish Medium Medium Medium
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, Journal Article, PUBLISHED  DOI
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 , Journal Article, PUBLISHED
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 , Journal Article, PUBLISHED  TARA - Full Text  DOI
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 , Journal Article, PUBLISHED  DOI
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 , Journal Article, PUBLISHED  DOI
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, Journal Article, PUBLISHED
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, Journal Article, PUBLISHED  DOI
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 , Journal Article, PUBLISHED  DOI
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, Journal Article, PUBLISHED
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 , Journal Article, PUBLISHED  DOI
  

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