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

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