Projects per year
- 1994-1998 B.Sc. in Microbiology, National University of Ireland Galway
- 1998-2000 M.Sc. (Res) in infectious diseases molecular diagnostics, National University of Ireland Galway
- 2003-2007 Ph.D. in the molecular diagnosis of Listeria species in food, National University of Ireland Galway
Prof O'Grady gained his B.Sc. in Microbiology, his M.Sc. (Res) in infectious diseases molecular diagnostics and his Ph.D. in molecular diagnosis of bacterial pathogens in food all at the National University of Ireland Galway (NUIG). He stayed at NUIG for his first post-doc, continuing his food microbiology research. This was followed by a two year stint in industry (Beckman Coulter) developing real-time PCR based molecular diagnostics assays for infectious diseases including Mycobacterium tuberculosis. Prof O’Grady then returned to academia, taking up a post-doc position at University College London on TB diagnostics. In January 2013 he was appointed Lecturer in Medical Microbiology at UEA, was promoted to Senior Lecturer in August 2016 and was promoted to Professor in Feb 2021. His research continues to focus on the molecular diagnosis of pathogens with the aim of translating this research broadly, in different sectors and diseases, to maximise community/patient benefit.
- 2006-2008 Postdoctoral Researcher at the National University of Ireland Galway
- 2008-2010 Research Scientist at Beckman Coulter
- 2010-2011 Research Associate at University College London
- 2011-2012 Senior Research Associate at University College London
- 2013-2016 Lecturer in Medical Microbiology at UEA
- 2016-2021 Senior Lecturer in Medical Microbiology at UEA
- 2018-present Group Leader at Quadram Institute Bioscience
- 2021-present Professor of Medical Microbiology at UEA
- Keynote speaker at '7th Annual New Zealand NGS Conference', New Zealand, 2015
- Plenary speaker at Oxford Nanopore 'London Calling' meeting, London, 2015
- Invited speaker at 'qPCR and NGS 2015' conference, Munich, 2015
- Founding and managing editor of a new Elsevier journal entitled “Biomolecular Detection and Quantification”, launched in 2014
- Expert panel member for GLOBVAC grant applications for the Norwegian government, 2015
- Expert panel member for grant applications to the German Federal Ministry of Education and Research (BMBF), 2013
- Peer review of Health Technology Assessment grant applications to the NIHR, UK, 2014
- Peer review of grant applications for the Belgian Science Policy Office (BELSPO), 2012
Key Research Interests and Expertise
In January 2013 I joined UEA where my research focusses on the molecular diagnosis of pathogens in complex clinical syndromes such as sepsis, respiratory tract infections and urinary tract infections. A particular focus is on the application of next generation sequencing in clinical diagnostics. Currently, NGS is being used in centralised national reference laboratories to type referred bacteria but is not yet used for routine diagnostic laboratories. Third generation NGS technology (eg real-time nanopore sequencing) will radically change this landscape, reducing cost and turnaround time and removing the need for expert operators and analysts. This will facilitate the use of NGS for the rapid, routine profiling of pathogens in clinical samples, possibly at the point-of-care. The main challenge to implementation remaining is sample preparation. Nucleic acid extraction is not optimised for the sequencing based detection of tiny amounts of pathogen nucleic acid in a vast excess of human nucleic acid, as applies, for example, in the investigation of bloodstream infection. We are facilitating the implementation of nanopore sequencing technology in clinical microbiology by developing nucleic acid extraction technologies for clinical samples containing low levels of pathogen (host DNA depletion and pathogen DNA enrichemnt methods) designed to make the sequencing based identification of pathogens and antibiotic resistances feasible.
Other research interests include PCR based molecular diagnostics, tuberculosis, global health, food microbiology and point-of-care diagnostics.
I welcome enquiries from motivated postdocs (or final year PhD students) who are interested in applying for their own postdoctoral fellowship funding to join my lab. I also welcome enquiries from self-funded PhD students.
Research Keywords: Molecular diagnostics, Real-time PCR, Sepsis, Respiratory tract infections, Next generation sequencing, Tuberculosis (NGS), Global health, Point of care, Medical microbiology, Food microbiology
Research Topics for PGR Supervision: Molecular diagnostics, Infectious diseases, Next generation sequencing based clinical diagnostics, PCR based diagnostics, Medical microbiology, Molecular epidemiology of infectious diseases, Pathogen detection in food, Infectious diseases and Global health, Tuberculosis
- Ashton, P.M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., and O'Grady, J. (2015). MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nature Biotechnology 33, 296-300.
- Bates M, O'Grady J (joint first author), Maeurer M, Tembo J, Chilukutu L, Chabala C, Kasonde R, Mulota P, Mzyece J, Chomba M et al: Assessment of the Xpert MTB/RIF assay for diagnosis of tuberculosis with gastric lavage aspirates in children in sub-Saharan Africa: a prospective descriptive study. Lancet Infect Dis 2013, 13(1):36-42.
- O'Grady J, Bates M, Chilukutu L, Mzyece J, Cheelo B, Chilufya M, Mukonda L, Mumba M, Tembo J, Chomba M et al: Evaluation of the Xpert MTB/RIF assay at a tertiary care referral hospital in a setting where tuberculosis and HIV infection are highly endemic. Clin Infect Dis 2012, 55(9):1171-1178.
- Bates M, O'Grady J (joint first author), Mwaba P, Chilukutu L, Mzyece J, Cheelo B, Chilufya M, Mukonda L, Mumba M, Tembo J et al: Evaluation of the burden of unsuspected pulmonary tuberculosis and co-morbidity with non-communicable diseases in sputum producing adult inpatients. PloS one 2012, 7(7):e40774.
- Reddington K, Zumla A, Bates M, van Soolingen D, Niemann S, Barry T, O'Grady J: SeekTB, a Two-Stage Multiplex Real-Time-PCR-Based Method for Differentiation of the Mycobacterium tuberculosis Complex. J Clin Microbiol 2012, 50(7):2203-2206.
- Reddington K, O'Grady J, Dorai-Raj S, Niemann S, van Soolingen D, Barry T: A novel multiplex real-time PCR for the identification of mycobacteria associated with zoonotic tuberculosis. PloS one 2011, 6(8):e23481.
- McGuinness S, McCabe E, O'Regan E, Dolan A, Duffy G, Burgess C, Fanning S, Barry T, O'Grady J: Development and validation of a rapid real-time PCR based method for the specific detection of Salmonella on fresh meat. Meat Sci 2009, 83(3):555-562.
- O' Grady J, Sedano-Balbas S, Maher M, Smith T, Barry T: Rapid real-time PCR detection of Listeria monocytogenes in enriched food samples based on the ssrA gene, a novel diagnostic target. Food Microbiol 2008, 25(1):75-84.
- O'Grady J, Lacey K, Glynn B, Smith TJ, Barry T, Maher M: tmRNA--a novel high-copy-number RNA diagnostic target--its application for Staphylococcus aureus detection using real-time NASBA. FEMS Microbiol Lett 2009, 301(2):218-223.
- Dimov IK, Garcia-Cordero JL, O'Grady J, Poulsen CR, Viguier C, Kent L, Daly P, Lincoln B, Maher M, O'Kennedy R et al: Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics. Lab Chip 2008, 8(12):2071-2078.
I take an active role in teaching both undergraduate and postgraduate students. I am currently primary supervisor of three PhD students and co-supervisor of two. I am a first year MBBS problem based learning (PBL) tutor, the second year Microbiology and Immunology student selected studies (SSS) lead tutor and an advisor for 5 MBBS students. I also provide laboratory based experience to MBBS students as part of the 'pathways to research' SSS theme.
Doctor of Philosophy, National University of Ireland, Maynooth
Award Date: 1 Jan 2007
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1/04/18 → 31/03/22
1/02/18 → 31/10/18
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance islandAshton, P., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J. & O'Grady, J., Mar 2015, In : Nature Biotechnology. 33, 3, p. 296–300 5 p.
Research output: Contribution to journal › ArticleFile243 Citations (Scopus)34 Downloads (Pure)
Assessment of the Xpert MTB/RIF Assay for Diagnosis of Tuberculosis with Gastric Lavage Aspirates in Children in Sub-Saharan Africa: A Prospective Descriptive StudyBates, M., O'Grady, J., Maeurer, M., Tembo, J., Chilukutu, L., Chabala, C., Kasonde, R., Mulota, P., Mzyece, J., Chomba, M., Mukonda, L., Mumba, M., Kapata, N., Rachow, A., Clowes, P., Hoelscher, M., Mwaba, P. & Zumla, A., 2013, In : The Lancet Infectious Diseases. 13, 1, p. 36-42 7 p.
Research output: Contribution to journal › Article107 Citations (Scopus)
Evaluation of the Xpert MTB/RIF Assay at a Tertiary Care Referral Hospital in a Setting Where Tuberculosis and HIV Infection Are Highly Endemic.O'Grady, J., Bates, M., Chilukutu, L., Mzyece, J., Cheelo, B., Chilufya, M., Mukonda, L., Mumba, M., Tembo, J., Chomba, M., Kapata, N., Maeurer, M., Rachow, A., Clowes, P., Hoelscher, M., Mwaba, P. & Zumla, A., 2012, In : Clinical Infectious Diseases. 55, 9, p. 1171-1178 8 p.
Research output: Contribution to journal › Article65 Citations (Scopus)
O'Grady, J., Poulsen, C. R., Viguier, C., Kent, L., Daly, P., Lincoln, B., Maher, M., O'Kennedy, R., Smith, T. J., Ricco, A. J. & Lee, L. P., 2008, In : Lab on a Chip. 8, 12, p. 2071-2078 8 p.
Research output: Contribution to journal › ArticleFile111 Citations (Scopus)13 Downloads (Pure)
SeekTB, A Two-Stage Multiplex Real-Time-PCR-Based Method for Differentiation of the Mycobacterium Tuberculosis Complex.Reddington, K., Zumla, A., Bates, M., van Soolingen, D., Niemann, S., Barry, T. & O'Grady, J., 2012, In : Journal of Clinical Microbiology. 50, 7, p. 2203-2206 4 p.
Research output: Contribution to journal › Article19 Citations (Scopus)