1. 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

  2. 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

  3. 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

  4. Published

    CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

    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: BioMed Central.

    Research output: Working paper

  5. Published

    CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

    Baker, D. J., Aydin, A., Le Viet, T., Kay, G. L., Rudder, S., de Oliveira Martins, L., Tedim, A. P., Kolyva, A., Diaz, M., Alikhan, N-F., Meadows, L., Bell, A., Gutierrez, A. V., Trotter, A. J., Thomson, N. M., Gilroy, R., Griffith, L., Adriaenssens, E. M., Stanley, R., Charles, I. & 9 others, Franslem-Elumogo, N., Wain, J., Prakash, R., Meader, E., Mather, A., Webber, M., Dervisevic, S., Page, A. J. & O'Grady, J., 9 Feb 2021, In : Genome Medicine. 13, 21.

    Research output: Contribution to journalArticle

  6. 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

  7. Published

    New Global Estimates of Malaria Deaths.

    Bates, M., O'Grady, J., Mudenda, V., Shibemba, A. & Zumla, A., 2012, In : The Lancet. 380, 9841, p. 560-561 2 p.

    Research output: Contribution to journalLetter

  8. 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

  9. 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

  10. 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

  11. Published

    Molecular Diagnosis of Active Pulmonary Tuberculosis.

    Bateson, A., Reddington, K. & O'Grady, J., 2012, Tuberculosis: Laboratory Diagnosis and Treatment Strategies. McHugh, T. (ed.). CABI Publishing

    Research output: Chapter in Book/Report/Conference proceedingChapter

  12. 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

  13. 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

  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

    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

  16. 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

  17. 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

  18. Published

    Surgery and Tuberculosis

    Cummings, I., O'Grady, J., Pai, V., Kolvekar, S. & Zumla, A., 2012, In : Current Opinion in Pulmonary Medicine. 18, 3, p. 241-245 5 p.

    Research output: Contribution to journalArticle

  19. 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

  20. Published

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

    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, In : Lab on a Chip. 8, 12, p. 2071-2078 8 p.

    Research output: Contribution to journalArticle

  21. 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

  22. 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

  23. Published

    Identification of Host-Specific Bacteroidales 16S rDNA Sequences from Human Sewage and Ruminant Feces

    Dorai-Raj, S., O'Grady, J., Cormican, M. & Colleran, E., 2011, In : Journal of Basic Microbiology. 52, 3, p. 277-284 8 p.

    Research output: Contribution to journalArticle

  24. Published
  25. Published

    New skeletal tuberculosis cases in past populations from Western Hungary (Transdanubia)

    Évinger, S., Bernert, Z., Fóthi, E., Wolff, K., Kővári, I., Marcsik, A., Donoghue, HD., O'Grady, J., Kiss, KK. & Hajdu, T., Jun 2011, In : HOMO - Journal of Comparative Human Biology. 62, 3, p. 165-183 19 p.

    Research output: Contribution to journalArticle

  26. Published

    Xpert MTB/RIF Test for Tuberculosis.

    Ferrara, G., O'Grady, J., Zumla, A. & Maeurer, M., 2011, In : The Lancet. 378, 9790, p. 482 1 p.

    Research output: Contribution to journalLetter

  27. Published

    Genomic diversity of Escherichia coli from healthy children in rural Gambia

    Foster-Nyarko, E., Alikhan, N-F., Ikumapayi, U. N., Sarwar, G., Okoi, C., Tientcheu, P-E. M., Defernez, M., O'Grady, J., Antonio, M. & Pallen, M. J., 6 Jan 2021, In : PeerJ. 9, e10572.

    Research output: Contribution to journalArticle

  28. Published

    Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

    Foster-Nyarko, E., Alikhan, N-F., Ravi, A., Thomson, N. M., Jarju, S., Kwambana-Adams, B. A., Secka, A., O'Grady, J., Antonio, M. & Pallen, M. J., Jan 2021, In : Microbial Genomics. 7, 1, 000484.

    Research output: Contribution to journalArticle

  29. Published

    Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

    Foster-Nyarko, E., Alikhan, N-F., Ravi, A., Thilliez, G., Thomson, N. M., Baker, D., Kay, G., Cramer, J. D., O'Grady, J., Antonio, M. & Pallen, M. J., Sep 2020, In : Microbial Genomics. 6, 9, 000428.

    Research output: Contribution to journalArticle

  30. Published

    Monolithic Centrifugal Microfluidic Platform for Bacteria Capture and Concentration, Lysis, Nucleic-Acid Amplification, and Real-Time Detection

    Garcia-Cordero, J. L., Dimov, I. K., O'Grady, J., Ducree, J., Barry, T. & Ricco, A. J., 2009, p. 356-359. 4 p.

    Research output: Contribution to conferencePaper

  31. Published

    Reusable Surface Plasmon Resonance Assay for the Specific Detection of Streptococcus Pneumoniae tmRNA.

    Glynn, B., Lacey, K., O'Grady, J., Barry, T., Smith, T. J. & Maher, M., Sep 2008, In : Journal of Rapid Methods & Automation in Microbiology. 16, 3, p. 210-221 12 p.

    Research output: Contribution to journalArticle

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. Published

    Extensively drug-resistant tuberculosis (XDR-TB) among health care workers in South Africa

    Jarand, J., Shean, K., O’Donnell, M., Loveday, M., Kvasnovsky, C., Van der Walt, M., Adams, S., Willcox, P., O'Grady, J., Zumla, A. & Dheda, K., 2010, In : Tropical Medicine & International Health. 15, 10, p. 1179-1184 6 p.

    Research output: Contribution to journalArticle

  40. 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

  41. 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

  42. Published

    Leprosy Trends in Zambia 1991-2009.

    Kapata, N., Chanda-Kapata, P., Grobusch, MP., O'Grady, J., Bates, M., Mwaba, P. & Zumla, A., 2012, In : Tropical Medicine & International Health. 17, 10, p. 1289-1293 5 p.

    Research output: Contribution to journalArticle

  43. Published

    Scale-up of TB and HIV Programme Collaborative Activities in Zambia - a 10-year Review

    Kapata, N., Chanda-Kapata, P., Grobusch, MP., O'Grady, J., Schwank, S., Bates, M., Jansenn, S., Mwinga, A., Cobelens, F., Mwaba, P. & Zumla, A., 2012, In : Tropical Medicine & International Health. 17, 6, p. 760-766 7 p.

    Research output: Contribution to journalArticle

  44. Published

    Trends of Zambia’s tuberculosis burden over the past two decades

    Kapata, N., Chanda-Kapata, P., O'Grady, J., Schwank, S., Bates, M., Mukonka, V., Zumla, A. & Mwaba, P., Nov 2011, In : Tropical Medicine & International Health. 16, 11, p. 1404-1409 6 p.

    Research output: Contribution to journalArticle

  45. 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

  46. Published
  47. Published

    Development and Validation of a Rapid Real-Time PCR Based Method for the Specific Detection of Salmonella on Fresh Meat

    McGuinness, S., McCabe, E., O’Regan, E., Dolan, A., Duffy, G., Burgess, C., Fanning, S., Barry, T. & O'Grady, J., 2009, In : Meat Science. 83, 3, p. 555-562 8 p.

    Research output: Contribution to journalArticle

  48. Published

    Tuberculosis diagnostics and biomarkers: needs, challenges, recent advances, and opportunities

    McNerney, R., Maeurer, M., Abubakar, I., Marais, B., Mchugh, T. D., Ford, N., Weyer, K., Lawn, S., Grobusch, M. P., Memish, Z., Squire, S. B., Pantaleo, G., Chakaya, J., Casenghi, M., Migliori, G-B., Mwaba, P., Zijenah, L., Hoelscher, M., Cox, H., Swaminathan, S. & 10 others, Kim, P. S., Schito, M., Harari, A., Bates, M., Schwank, S., O'Grady, J., Pletschette, M., Ditui, L., Atun, R. & Zumla, A., 2012, In : Journal of Infectious Diseases. 205, suppl 2, p. S147-S158 12 p.

    Research output: Contribution to journalLiterature review

  49. Published

    Screening of immigrants in the UK for latent tuberculosis

    McNerney, R., Ferrara, G., O'Grady, J., Maeurer, M. & Zumla, A., 2011, In : Expert Review of Respiratory Medicine. 5, 4, p. 483-486 4 p.

    Research output: Contribution to journalLiterature review

  50. Published

    Review of multidrug-resistant and extensively drug-resistant TB: global perspectives with a focus on sub-Saharan Africa

    Migliori, G. B., Dheda, K., Centis, R., Mwaba, P., Bates, M., O'Grady, J., Hoelscher, M. & Zumla, A., 2010, In : Tropical Medicine & International Health. 15, 9, p. 1052-1066 15 p.

    Research output: Contribution to journalLiterature review

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