Biography

Dr 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. Dr 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 and was promoted to Senior Lecturer in August 2016. 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.

Career History

  • 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-Present   Senior Lecturer in Medical Microbiology at UEA

Academic Background

  • 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

Highlighted Publications

See All

Ashton, P., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., O'Grady, J.

(2015)

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island,

in Nature Biotechnology

33.

pp. 296–300

Full Text UEA Repository

(Article)

(Published)


Bates, 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)

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.,

in The Lancet Infectious Diseases

13.

pp. 36-42

Full Text UEA Repository

(Article)

(Published)


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)

Evaluation of the Xpert MTB/RIF Assay at a Tertiary Care Referral Hospital in a Setting Where Tuberculosis and HIV Infection Are Highly Endemic.,

in Clinical Infectious Diseases

55.

pp. 1171-1178

Full Text UEA Repository

(Article)

(Published)


Reddington, K., Zumla, A., Bates, M., van Soolingen, D., Niemann, S., Barry, T., O'Grady, J.

(2012)

SeekTB, A Two-Stage Multiplex Real-Time-PCR-Based Method for Differentiation of the Mycobacterium Tuberculosis Complex.,

in Journal of Clinical Microbiology

50.

pp. 2203-2206

Full Text UEA Repository

(Article)

(Published)


Dimov, I. K., Garcia-Cordero, J. L., 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)

Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics.,

in Lab on a Chip

8.

pp. 2071-2078

Full Text UEA Repository

(Article)

(Published)


All Publications

See Highlights
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Ozongwu, C., Personne, Y., Platt, G., Jeanes, C., Aydin, S., Kozato, N., Gant, V., O'Grady, J., Enne, V.

(2017)

The Unyvero P55 ‘sample-in, answer-out’ pneumonia assay: A performance evaluation,

in Biomolecular Detection and Quantification

13

pp. 1-6

Full Text UEA Repository

(Article)

(Published)


Polepole, P., Kabwe, M., Kasonde, M., Tembo, J., Shibemba, A., O'Grady, J., Kapata, N., Zumla, A., Bates, M.

(2017)

Performance of the Xpert MTB/RIF assay in the diagnosis of tuberculosis in formalin-fixed, paraffin-embedded tissues,

in International Journal of Mycobacteriology

6

(1)

pp. 87-93

Full Text UEA Repository

(Article)

(Published)


Wain, J., O'Grady, J.

(2017)

Genomic Diversity in Salmonella enterica,

in Applied Genomics of Foodborne Pathogens.

Springer International Publishing

pp. 91-107

ISBN 978-3-319-43749-1

Full Text

(Other chapter contribution)

(Published)


Schmidt, K., Mwaigwisya, S., Crossman, L. C., Doumith, M., Munroe, D., Pires, C., Khan, A. M., Woodford, N., Saunders, N. J., Wain, J., O'Grady, J., Livermore, D. M.

(2017)

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing,

in Journal of Antimicrobial Chemotherapy

72

(1)

pp. 104-114

Full Text UEA Repository

(Article)

(Published)


Phelan, J., O’Sullivan, D. M., Machado, D., Ramos, J., Whale, A. S., O'Grady, J., Dheda, K., Campino, S., McNerney, R., Viveiros, M., Huggett, J. F., Clark, T. G.

(2016)

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs,

in Genome Medicine

8

article no. 132

Full Text UEA Repository

(Article)

(Published)


Jeanes, C., O'Grady, J.

(2016)

Diagnosing tuberculosis in the 21st century – Dawn of a genomics revolution?,

in International Journal of Mycobacteriology

5

(4)

pp. 384-391

Full Text UEA Repository

(Article)

(Published)


Ip, C. L., Loose, M., Tyson, J. R., de Cesare, M., Brown, B. L., Jain, M., Leggett, R. M., Eccles, D. A., Zalunin, V., Urban, J. M., Piazza, P., Bowden, R. J., Paten, B., Mwaigwisya, S., Batty, E. M., Simpson, J. T., Snutch, T. P., Birney, E., Buck, D., Goodwin, S., Jansen, H. J., O'Grady, J., Olsen, H. E.

(2015)

MinION Analysis and Reference Consortium: Phase 1 data release and analysis,

in F1000Research

4

(1075)

article no. 1075

Full Text UEA Repository

(Article)

(Published)


Donoghue, H. D., Spigelman, M., O'Grady, J., Szikossy, I., Pap, I., Lee, O. Y., Wu, H. H. T., Besra, G. S., Minnikin, D. E.

(2015)

Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy,

in Tuberculosis

95

(1)

pp. S140-S144

Full Text UEA Repository

(Article)

(Published)


Mwaigwisya, S., Assiri, R. A. M., O'Grady, J.

(2015)

Emerging commercial molecular tests for the diagnosis of bloodstream infection,

in Expert Review of Molecular Diagnostics

15

(5)

pp. 681-692

Full Text UEA Repository

(Article)

(Published)


Donoghue, H. D., Michael Taylor, G., Marcsik, A., Molnár, E., Pálfi, G., Pap, I., Teschler-Nicola, M., Pinhasi, R., Erdal, Y. S., Velemínsky, P., Likovsky, J., Belcastro, M. G., Mariotti, V., Riga, A., Rubini, M., Zaio, P., Besra, G. S., Lee, O. Y., Wu, H. H. T., Minnikin, D. E., Bull, I. D., O'Grady, J., Spigelman, M.

(2015)

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe,

in Infection, Genetics and Evolution

31

pp. 250-256

Full Text UEA Repository

(Article)

(Published)


O'Grady, J., Kik, S. V., Ferrara, G.

(2015)

Extra-pulmonary tuberculosis and Xpert® MTB/RIF: all about meta-analyses?,

in International Journal of Tuberculosis and Lung Disease

19

(3)

pp. 254

Full Text UEA Repository

(Article)

(Published)


Ashton, P., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., O'Grady, J.

(2015)

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island,

in Nature Biotechnology

33

(3)

pp. 296–300

Full Text UEA Repository

(Article)

(Published)


Huggett, J., O'Grady, J., Bustin, S.

(2015)

qPCR, dPCR, NGS – A journey,

in Biomolecular Detection and Quantification

3

pp. A1-A5

Full Text

(Editorial)

(Published)


Kroidl, I., Clowes, P., Reither, K., Rojas-Ponce, G., Ntinginya, E. N., Kalomo, M., Minja, L. T., Kowuor, D., Saathoff, E., Kroidl, A., Heinrich, N., Maboko, L., Bates, M., O'Grady, J., Zumla, A., Hoelscher, M., Rachow, A.

(2015)

Performance of urine lipoarabinomannan assays for paediatric tuberculosis in Tanzania,

in European Respiratory Journal

46

(3)

pp. 761-770

Full Text UEA Repository

(Article)

(Published)


Huggett, J., O'Grady, J., Bustin, S.

(2014)

How to make Mathematics Biology's next and better microscope,

in Biomolecular Detection and Quantification

1

(1)

pp. A1-A3

Full Text UEA Repository

(Article)

(Published)


O'Grady, J. (ed.), Huggett, J. (ed.)

(2014)

Molecular Diagnostics: Current Research and Applications,

Caister Academic Press

ISBN 978-1-908230-41-6

UEA Repository

(Book)

(Published)


Huggett, J., Dorai-Raj, S., Falinska, A., O'Grady, J.

(2014)

Molecular Diagnostics: An Introduction,

in Molecular Diagnostics: Current Research and Applications.

Caister Academic Press

UEA Repository

(Chapter)

(Published)


Clancy, E., Reddington, K., Barry, T., Huggett, J., O'Grady, J.

(2014)

Future of Molecular Diagnostics: The Example of Infectious Diseases,

in Molecular Diagnostics: Current Research and Applications.

Caister Academic Press

UEA Repository

(Chapter)

(Published)


Bates, M., Ahmed, Y., Chilukutu, L., Tembo, J., Cheelo, B., Sinyangwe, S., Kapata, N., Maeurer, M., O'Grady, J., Mwaba, P., Zumla, A.

(2013)

Use of the Xpert MTB/RIF assay for diagnosing pulmonary tuberculosis comorbidity and multidrug-resistant TB in obstetrics and gynaecology inpatient wards at the University Teaching Hospital, Lusaka, Zambia,

in Tropical Medicine & International Health

18

(9)

pp. 1134-40

Full Text UEA Repository

(Article)

(Published)


Bates, 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)

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.,

in The Lancet Infectious Diseases

13

(1)

pp. 36-42

Full Text UEA Repository

(Article)

(Published)


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Key Research Interests

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

Selected Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

Teaching Interests

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.

External Activities and Indicators of Esteem

  • 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