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.

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