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.