1. 2020
  2. Published
  3. Published

    CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

    Baker, D. J., Kay, G. L., Aydin, A., Le-Viet, T., Rudder, S., Tedim, A. P., Kolyva, A., Diaz, M., de Oliveira Martins, L., Alikhan, N-F., Meadows, L., Bell, A., Gurierrez, A. V., Trotter, A. J., Thomson, N. M., Gilroy, R., Griffith, L., Adriaenssens, E. M., Stanley, R., Charles, I. G. & 9 others, Elumogo, N., Wain, J., Prakash, R., Meader, E., Mather, A. E., Webber, M. A., Dervisevic, S., Page, A. J. & O'Grady, J., 24 Jun 2020, BioRxiv: biorxiv.

    Research output: Working paper

  4. Published

    Rapid and Point-of-Care Testing in Respiratory Tract Infections: An Antibiotic Guardian?

    Dhesi, Z., Enne, V. I., O'Grady, J., Gant, V. & Livermore, D. M., 12 Jun 2020, In : ACS Pharmacology & Translational Science. 3, 3, p. 401-417 17 p.

    Research output: Contribution to journalReview article

  5. Published

    Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

    Reddington, K., Eccles, D., O'Grady, J., Drown, D. M., Hansen, L. H., Nielsen, T. K., Ducluzeau, A-L., Leggett, R. M., Heavens, D., Peel, N., Snutch, T. P., Bayega, A., Oikonomopoulos, S., Ragoussis, I., Barry, T., van der Helm, E., Jolic, D., Richardson, H., Jansen, H., Tyson, J. R. & 2 others, Jain, M. & Brown, B. L., 10 Jun 2020, In : GigaScience. 9, 6, giaa053.

    Research output: Contribution to journalArticle

  6. Published

    Preliminary evaluation of a rapid lateral flow calprotectin test for the diagnosis of prosthetic joint infection

    Trotter, A. J., Dean, R., Whitehouse, C. E., Mikalsen, J., Hill, C., Brunton-Sim, R., Kay, G. L., Shakokani, M., Durst, A. Z. E., Wain, J., Mcnamara, I. & O’Grady, J., 5 May 2020, In : Bone and Joint Research. 9, 5, p. 202-210 9 p.

    Research output: Contribution to journalArticle

  7. Published

    Co-infections: potentially lethal and unexplored in COVID-19

    Cox, M. J., Loman, N., Bogaert, D. & O'Grady, J., May 2020, In : The Lancet Microbe. 1, 1, 1 p., e11.

    Research output: Contribution to journalComment/debate

  8. Published

    Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

    Brinda, K., Callendrello, A., Ma, K. C., MacFadden, D. R., Charalampous, T., Lee, R. S., Cowley, L., Wadsworth, C. B., Grad, Y. H., Kucherov, G., O'Grady, J., Baym, M. & Hanage, W. P., Mar 2020, In : Nature Microbiology. 5, 3, p. 455-464 10 p.

    Research output: Contribution to journalArticle

  9. Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

    Street, T. L., Barker, L., Sanderson, N. D., Kavanagh, J., Hoosdally, S., Cole, K., Newnham, R., Selvaratnam, M., Andersson, M., Llewelyn, M. J., O'Grady, J., Crook, D. W. & Eyre, D. W., 24 Feb 2020, In : Journal of Clinical Microbiology. 58, 3, 13 p., e01822-19.

    Research output: Contribution to journalArticle

  10. 2019
  11. Published

    Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

    Yang, L., Haidar, G., Zia, H., Nettles, R., Qin, S., Wang, X., Shah, F., Rapport, S. F., Charalampous, T., Methé, B., Fitch, A., Morris, A., McVerry, B. J., O'Grady, J. & Kitsios, G. D., 27 Nov 2019, In : Respiratory Research. 20, 1, p. 265

    Research output: Contribution to journalArticle

  12. Published

    Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance

    Trotter, A. J., Aydin, A., Strinden, M. J. & O’grady, J., 1 Oct 2019, In : Current Opinion in Microbiology. 51, p. 39-45

    Research output: Contribution to journalReview article

  13. Published

    Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

    Phelan, J. E., O'Sullivan, D. M., Machado, D., Ramos, J., Oppong, Y. E. A., Campino, S., O'Grady, J., McNerney, R., Hibberd, M. L., Viveiros, M., Huggett, J. F. & Clark, T. G., 24 Jun 2019, In : Genome Medicine. 11, 1, 41.

    Research output: Contribution to journalArticle

  14. Published

    Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

    Charalampous, T., Kay, G., Richardson, H., Aydin, A., Baldan, R., Jeanes, C., Rae, D., Grundy, S., Turner, D. J., Wain, J., Leggett, R. M., Livermore, D. & O'Grady, J., 24 Jun 2019, In : Nature Biotechnology. 37, p. 783–792

    Research output: Contribution to journalArticle

  15. Published

    Metagenomic Sequencing of Respiratory Microbial Communities for Detection of Etiologic Pathogens of Pneumonia in Mechanically-Ventilated Adult Patients

    Nettles, R., Yang, L., Qin, S., Bednash, J. S., Fitch, A., Evankovich, J., Bain, W., Dunlap, D. G., Shah, F., Rapport, S., Lee, J., Morris, A., McVerry, B. J., O'Grady, J. & Kitsios, G., May 2019.

    Research output: Contribution to conferenceAbstract

  16. Published

    Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines

    Schmidt, K., Stanley, K. K., Hale, R., Smith, L., Wain, J., O'Grady, J. & Livermore, D. M., 1 Feb 2019, In : Journal of Antimicrobial Chemotherapy. 74, 2, p. 349–356 8 p.

    Research output: Contribution to journalArticle

  17. Published

    A powerful, non-invasive test to rule out infection

    O’Grady, J., 2019, In : Nature Microbiology. 4, 4, p. 554-555 2 p.

    Research output: Contribution to journalComment/debate

  18. 2018
  19. Published

    Leprosy at the edge of Europe—Biomolecular, isotopic and osteoarchaeological findings from medieval Ireland

    Taylor, G. M., Murphy, E. M., Mendum, T. A., Pike, A. W. G., Linscott, B., Wu, H., O’Grady, J., Richardson, H., O’Donovan, E., Troy, C. & Stewart, G. R., 26 Dec 2018, In : PLoS One. 13, 12, e0209495.

    Research output: Contribution to journalArticle

  20. Published

    Nanopore sequencing and assembly of a human genome with ultra-long reads

    Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olson, H. E., Pedersen, B. S., Rhie, A., Richardson, H., Quinlan, A. R., Snutch, T. P. & 6 others, Tee, L., Paten, B., Phillippy, A. M., Simpson, J. T., Loman, N. J. & Loose, M., Jan 2018, In : Nature Biotechnology. 36, p. 338–345 8 p.

    Research output: Contribution to journalArticle

  21. Published

    Diagnosis of Lower Respiratory Tract Infections using nanopore sequencing

    Charalampous, T., Richardson, H., Kay, G., Baldan, R., Jeanes, C., Turner, D., Wain, J., Livermore, D., Leggett, R. & O'Grady, J., 2018, In : European Respiratory Journal. 52, 2 p., PA5308.

    Research output: Contribution to journalAbstract

  22. Published

    The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

    Angers-Loustau, A., Petrillo, M., Bengtsson-Palme, J., Berendonk, T., Blais, B., Chan, K-G., Coque, T. M., Hammer, P., Heß, S., Kagkli, D. M., Krumbiegel, C., Lanza, V. F., Madec, J-Y., Naas, T., O'Grady, J., Paracchini, V., Rossen, J. W. A., Ruppé, E., Vamathevan, J., Venturi, V. & 1 others, Van den Eede, G., 2018, In : F1000Research. 7

    Research output: Contribution to journalReview article

  23. 2017
  24. Published

    Diagnosing antimicrobial resistance

    Burnham, C-A. D., Leeds, J., Nordmann, P., O'Grady, J. & Patel, J., 12 Oct 2017, In : Nature Reviews Microbiology. 15, 11, p. 697-703 7 p.

    Research output: Contribution to journalReview article

  25. Published

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

    Ozongwu, C., Personne, Y., Platt, G., Jeanes, C., Aydin, S., Kozato, N., Gant, V., O'Grady, J. & Enne, V. I., Sep 2017, In : Biomolecular Detection and Quantification. 13, p. 1-6 6 p.

    Research output: Contribution to journalArticle

  26. Published

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

    Polepole, P., Kabwe, M., Kasonde, M., Tembo, J., Shibemba, A., O'Grady, J., Kapata, N., Zumla, A. & Bates, M., 10 Mar 2017, In : International Journal of Mycobacteriology. 6, 1, p. 87-93 7 p.

    Research output: Contribution to journalArticle

  27. Published

    Genomic Diversity in Salmonella enterica

    Wain, J. & O'Grady, J., 24 Jan 2017, Applied Genomics of Foodborne Pathogens. Deng, X., den Bakker, H. C. & Hendriksen, R. S. (eds.). Springer, p. 91-107 Chapter 6. (Food Microbiology and Food Safety).

    Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

  28. Published

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

    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., 1 Jan 2017, In : Journal of Antimicrobial Chemotherapy. 72, 1, p. 104-114 11 p.

    Research output: Contribution to journalArticle

  29. 2016
  30. Published

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

    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., 22 Dec 2016, In : Genome Medicine. 8, 132.

    Research output: Contribution to journalArticle

  31. Published

    Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection

    Bates, M., Polepole, P., Kapata, N., Loose, M. & O'Grady, J., Dec 2016, In : International Journal of Mycobacteriology. 5 Suppl 1, p. S24

    Research output: Contribution to journalArticle

  32. Published

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

    Jeanes, C. & O'Grady, J., Dec 2016, In : International Journal of Mycobacteriology. 5, 4, p. 384-391 8 p.

    Research output: Contribution to journalArticle

  33. 2015
  34. Published

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

    Ip, C. L. C., 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. & 3 others, Jansen, H. J., O'Grady, J. & Olsen, H. E., 15 Oct 2015, In : F1000Research. 4, 1075, 1075.

    Research output: Contribution to journalArticle

  35. Published

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

    Donoghue, H. D., Spigelman, M., O'Grady, J., Szikossy, I., Pap, I., Lee, O. Y-C., Wu, H. H. T., Besra, G. S. & Minnikin, D. E., Jun 2015, In : Tuberculosis. 95, 1, p. S140-S144

    Research output: Contribution to journalArticle

  36. Published

    Emerging commercial molecular tests for the diagnosis of bloodstream infection

    Mwaigwisya, S., Assiri, R. A. M. & O'Grady, J., May 2015, In : Expert Review of Molecular Diagnostics. 15, 5, p. 681-692 12 p.

    Research output: Contribution to journalArticle

  37. Published

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

    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-C., Wu, H. H. T., Minnikin, D. E. & 3 others, Bull, I. D., O'Grady, J. & Spigelman, M., Apr 2015, In : Infection, Genetics and Evolution. 31, p. 250-256 7 p.

    Research output: Contribution to journalArticle

  38. Published

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

    O'Grady, J., Kik, S. V. & Ferrara, G., 1 Mar 2015, In : International Journal of Tuberculosis and Lung Disease. 19, 3, p. 254 1 p.

    Research output: Contribution to journalArticle

  39. Published

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

    Ashton, 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 journalArticle

  40. Published

    qPCR, dPCR, NGS – A journey

    Huggett, J., O'Grady, J. & Bustin, S., Mar 2015, In : Biomolecular Detection and Quantification. 3, p. A1-A5

    Research output: Contribution to journalEditorial

  41. Published

    Performance of urine lipoarabinomannan assays for paediatric tuberculosis in Tanzania

    Kroidl, I., Clowes, P., Reither, K., Mtafya, B., 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, In : European Respiratory Journal. 46, 3, p. 761-770 10 p.

    Research output: Contribution to journalArticle

  42. 2014
  43. Published

    How to make Mathematics Biology's next and better microscope

    Huggett, J., O'Grady, J. & Bustin, S., Sep 2014, In : Biomolecular Detection and Quantification. 1, 1, p. A1-A3

    Research output: Contribution to journalArticle

  44. Published

    Future of Molecular Diagnostics: The Example of Infectious Diseases

    Clancy, E., Reddington, K., Barry, T., Huggett, J. & O'Grady, J., 1 May 2014, Molecular Diagnostics: Current Research and Applications. Caister Academic Press

    Research output: Chapter in Book/Report/Conference proceedingChapter

  45. Published

    Molecular Diagnostics: An Introduction

    Huggett, J., Dorai-Raj, S., Falinska, A. & O'Grady, J., 1 May 2014, Molecular Diagnostics: Current Research and Applications. Caister Academic Press

    Research output: Chapter in Book/Report/Conference proceedingChapter

  46. Published

    Molecular Diagnostics: Current Research and Applications

    O'Grady, J. (ed.) & Huggett, J. (ed.), 1 May 2014, Norwich, UK: Caister Academic Press.

    Research output: Book/ReportBook

  47. 2013
  48. Published

    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

    Bates, M., Ahmed, Y., Chilukutu, L., Tembo, J., Cheelo, B., Sinyangwe, S., Kapata, N., Maeurer, M., O'Grady, J., Mwaba, P. & Zumla, A., Sep 2013, In : Tropical Medicine & International Health. 18, 9, p. 1134-40 7 p.

    Research output: Contribution to journalArticle

  49. Published

    Advances in Multiparametric Molecular Diagnostics Technologies for Respiratory Tract Infections

    Reddington, K., Tuite, N., Barry, T., O'Grady, J. & Zumla, A., 2013, In : Current Opinion in Pulmonary Medicine. 19, 3, p. 298-304 7 p.

    Research output: Contribution to journalLiterature review

  50. Published

    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

    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, In : The Lancet Infectious Diseases. 13, 1, p. 36-42 7 p.

    Research output: Contribution to journalArticle

  51. Published

    Evaluation of a Novel Listeria Enrichment Broth Combined with a Real-Time PCR Diagnostics Assay for the Specific Detection of Listeria Monocytogenes in RTE Pork Products

    Gómez, D., McGuinness, S., Reddington, K., O'Grady, J., Yangüela, J. & Barry, T., 2013, In : International Journal of Food Science & Technology. 48, 5, p. 1103-1108

    Research output: Contribution to journalArticle

  52. Published

    Trends in Childhood Tuberculosis in Zambia: A Situation Analysis

    Kapata, N., Chanda-Kapata, P., O'Grady, J., Bates, M., Mwaba, P., Janssen, S., Marais, B., Cobelens, F., Grobusch, M. & Zumla, A., 2013, In : Journal of Tropical Pediatrics. 59, 2, p. 134-139 6 p.

    Research output: Contribution to journalArticle

  53. 2012
  54. Published

    Evaluation of the burden of unsuspected pulmonary tuberculosis and co-morbidity with non-communicable diseases in sputum producing adult inpatients

    Bates, M., O'Grady, J., Mwaba, P., Chilukutu, L., Mzyece, J., Cheelo, B., Chilufya, M., Mukonda, L., Mumba, M., Tembo, J., Chomba, M., Kapata, N., Rachow, A., Clowes, P., Maeurer, M., Hoelscher, M. & Zumla, A., 27 Jul 2012, In : PLoS One. 7, 7, e40774.

    Research output: Contribution to journalArticle

  55. Published

    Tuberculosis Trends in Saudis and Non-Saudis in the Kingdom of Saudi Arabia – A 10 Year Retrospective Study (2000–2009).

    Abouzeid, M. S., Zumla, A. I., Felemban, S., Alotaibi, B., O'Grady, J. & Memish, Z. A., 20 Jun 2012, In : PLoS One. 7, 6, e39478.

    Research output: Contribution to journalArticle

  56. Published

    Chest Radiography for Tuberculosis Screening is Back on the Agenda

    Iademarco, M. F., O'Grady, J. & Lönnroth, K., 2012, In : International Journal of Tuberculosis and Lung Disease. 16, 11, p. 1421-1422 2 p.

    Research output: Contribution to journalEditorial

  57. Published
  58. Published

    Drug-Resistant Tuberculosis--Current Dilemmas, Unanswered Questions, Challenges and Priority Needs

    Zumla, A., Abubakar, I., Raviglione, M., Hoelscher, M., Ditiu, L., Mchugh, T. D., Squire, S. B., Cox, H., Ford, N., McNerney, R., Marais, B., Grobusch, M., Lawn, S. D., Migliori, G-B., Mwaba, P., O'Grady, J., Pletschette, M., Ramsay, A., Chakaya, J., Schito, M. & 4 others, Swaminathan, S., Memish, Z., Maeurer, M. & Atun, R., 2012, In : Journal of Infectious Diseases. 205, suppl 2, p. S228-S240 13 p.

    Research output: Contribution to journalLiterature review

  59. Published

    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 journalArticle

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