Dr. Peter Flanagan

Dr. Peter Flanagan

Visiting Research Fellow, Clinical Microbiology


Currently, I am appointed as a Clinical Scientist to the Irish Mycobacteria Reference Laboratory (IMRL) at St. James's Hospital Dublin. I have a number of years of research experience spanning Ireland and the UK in the field of molecular microbiology and virology. My qualifications include a BSc in Biological Sciences, an MSc in Molecular Biology and Pathology of Viruses and a PhD in Molecular Microbiology. Throughout my undergraduate degree, I have chosen elective subjects such as immunology, advanced immunology and applied immunology as well as molecular biology and microbiology. 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, Short Pulse Anti-Retroviral Therapy at Seroconversion. In 2011 I secured a place to complete a Masters in Virology at Imperial College London. Here, I further developed and advanced my technical ability and knowledge of molecular biology, more specifically RNA silencing. Shortly later, I successfully secured a place to complete a PhD in molecular microbiology of the fungal pathogen Candida albicans at the Dublin Dental University Hospital, Trinity College Dublin. My PhD saw me utilize techniques that included, but were not limited to, gene manipulation, cloning and knockouts using the SAT1 cassette and CRISPR Cas methods. Moreover, I performed RNAseq, cell culture and infection assays within cell lines and in vivo with the wax moth larva Galleria mellonella. Upon completion of my PhD, I was appointed to research fellow and pioneered the implementation of 3rd generation sequencing within the molecular microbiology group using Oxford Nanopore Technologies. In addition to teaching laboratory techniques, I developed the required bioinformatic command line analysis required by the molecular microbiology group. In addition to research activities, I lectured immunology to the 1st year Dental nurses and acted as a problem-based learning tutor to 1st year Dental students. This involved 6 hours of tutorials seeing me multitask research and teaching commitments as well as managing undergraduate students as part of their final year research project. In addition, I 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. Currently, my role is to stimulate a research and development environment as well as participate in method development and implementation of new techniques and writing standard operating procedures. A key aspect of my role is to develop and deploy whole genome sequencing (WGS) and a bioinformatic pipeline for the rapid identification of Mycobacterium tuberculosis recovered from patient samples and determining the drug susceptibility profile. This involves the Illumina MiSeq and Oxford Nanopore MinION platforms. Moreover, I have developed a Microsoft Access database for inputting genomic data and generating reports. In addition, I collaborate with the National MRSA Reference Laboratory. Both laboratories wish to implement WGS as a means to identify drug resistance and more importantly, identify the relatedness amongst isolates during an outbreak. I have developed the bioinformatic analysis work flows for both reference laboratories and taught staff how to use these command line tools. The development of WGS has resulted in interdisciplinary collaboration across the hospital. This includes the IT department in order to develop and implement a new and novel network for the analysis of WGS data. In addition, the clinical microbiology department have recruited me to perform and develop WGS for other organisms including C. difficle, C. parapsilosis and P. aeruginosa.

Publications and Further Research Outputs

  • 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, p6346-6351Journal Article, 2017, DOI
  • 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), 2017Journal Article, 2017, DOI
  • 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, p54Journal Article, 2011
  • 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--1485Journal Article, 2010
  • 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, pe1004914Journal Article, 2015
  • 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--323Journal Article, 2013
  • 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), 2018Journal Article, 2018, DOI , URL , TARA - Full Text
  • 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, 2020Journal Article, 2020
  • 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, 2021Journal Article, 2021, 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), 2021Journal Article, 2021
  • 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, p51-53Journal Article, 2019, 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, pdlab101Journal Article, 2021, DOI