Prof Matthew Holden

Prof Matthew Holden

Director of Impact

Professor

Phone
+44 (0)1334 46 3504
Email
mtgh@st-andrews.ac.uk

 

Research areas

I am a molecular microbiologist and computer biologist with an interest in pathogenomics and the application of genomics in public health. I have over 24 years’ experience in bacterial whole genome sequencing (WGS), 13 of which were as a member of Pathogen Sequencing Unit at The Wellcome Trust Sanger Institute, responsible for sequencing and analysis of the genomes of a wide range of microbial pathogens. Since moving to the University of 58³Ô¹Ï in 2013, I have established a translational genomics research group working closely with academic, NHS and public health partners. My work has focused on using WGS as a research tool to investigate the evolution of pathogens and their ability to cause disease, and also as a clinical tool to identify outbreaks and trace the spread of infectious diseases. I have acted as the genomics lead for the CSO funded SHAIPI consortium tackling nosocomial infections in Scotland and led NIHR funded HATUA and CARE consortia investigating the burden and drivers of antibacterial resistance (ABR) and impact of COVID-19 on ABR in East Africa.

PhD supervision

  • Sepideh Benvari
  • Madeleine Clarkson
  • Ashley Deventer
  • Eva Agnes Laker Odongpiny

Selected publications

  • Open access
    Rivas Ramos, J. E., Johnston, P. R., Hammond, R. J. H., Holden, M. T. G., Sloan, D. J. & Haag, A. F., 28 Jan 2026, In: Access Microbiology. 8, 1, p. 1-4 4 p., 001110.v3.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Chalka, A., Crozier, L., Vallejo-Trujillo, A., Low, A., McAteer, S., Qarkaxhija, V., Templeton, K., Tongue, S. C., Evans, J., Foster, G., Webster, C., Evans, T., Marwick, C. A., Raza, A., Parcell, B. J., Holden, M. T. G., McNeilly, T., Fitzgerald, S., Mitchell, M. & Silva, N. & 18 others, Robertshaw-McFarlane8, E., Hamilton, S., Wells, B., Hamilton, C., Watson, E., Finlay, D., Bolland, J., Redshaw, J., Walker, D., Heywood, J., King, C., Baker-Austin, C., Papadopoulou, A., Powell, A., Morgan, G., Paterson, G. K., McElhiney, J. & Gally, D. L., 20 Apr 2026, (E-pub ahead of print) In: Microbial Genomics. 12, 4, 001693.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Odongpiny, E. L. A., Otaalo, B., Musaazi, J., Nalugga, E. A., Kiguba, R., Ngabirano, D., Ddungu, A., Owarwo, N., Kesby, M., Holden, M., Castelnuovo, B., Semeere, A., Sloan, D. J. & Sekaggya, C., 7 May 2026, (E-pub ahead of print) In: AIDS. Ahead of Print

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Laker Odongpiny, E. A., Nicol, M., Katana, E., Owori, J., Buzibye, A., Sedan, K., Kesby, M., Holden, M., Owarwo, N., Meya, D., Castelnuovo, B., Sloan, D. J. & Sekaggya, C., 24 Jan 2025, (E-pub ahead of print) In: HIV Medicine. Early View, 14 p.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Gupta, R. & Holden, M., 1 May 2025, (E-pub ahead of print) In: Cureus: Journal of Medical Science. 17, 5, e83307.

    Research output: Contribution to journal › Review article › peer-review

  • Open access
    Williams, D. J., Hawkins, A., Hernandez, R. E., Mariano, G., Mathers, K., Buchanan, G., Stonier, B. J., Inkster, T., Leanord, A., Chalmers, J. D., Thomson, N. R., Holden, M. T. G. & Coulthurst, S. J., 12 Feb 2025, In: Cell Host & Microbe. 33, 2, p. 252-266.E5 20 p.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Wei, K. C., Purushothaman, S., Azzato, F., Baker, K. S., Birkeland, K. W., Brunet, S., Campos, J., Connor, T. R., Giske, C. G., Greub, G., Hallbäck, E. T., Harmsen, D., Hodcroft, E. B., Holden, M. T. G., Jacob, J., Kahles, A., Lagos, A. C., Lipworth, S., Loo, E. & Miotto, P. & 15 others, Neher, R. A., Neves, A., Ready, D., Roloff, T., Rooney, A., Rousseau, E., Schrenzel, J., Sundqvist, M., Viegas, S., Wegner, F., Aamot, H. V., Niemann, S., Williamson, D. A., Mölling, P. & Egli, A., 23 Oct 2025, In: Microbes and Infection. 27, 7, p. 1-8 8 p., 105557.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    McHugh, M. P., Horsfield, S. T., von Wachsmann, J., Toussaint, J., Pettigrew, K. A., Czarniak, E., Evans, T. J., Leanord, A., Tysall, L., Gillespie, S. H., Templeton, K. E., Holden, M. T. G., Croucher, N. J. & Lees, J. A., 28 Apr 2025, In: Microbial Genomics. 11, 4, p. 1-9 9 p., 001404.

    Research output: Contribution to journal › Article › peer-review

  • Open access
    Ke, X., Smith, V. A., Mshana, S. E., Asiimwe, B., Neema, S., Kiiru, J., Mushi, M. F., Mmbaga, B. T., Mwanga, J. R., Kibiki, G., Stelling, J., Gillespie, S. H., Green, D. L., Benvari, S., Sabiiti, W., Kesby, M., Lynch, A. G., Sandeman, A., Sloan, D. J. & Holden, M. T. & 2 others, Keenan, K. & HATUA Consortium, 4 Feb 2025, Research Square.

    Research output: Working paper › Preprint

  • Open access
    David, S., Caballero, J. D., Couto, N., Abudahab, K., Alikhan, N.-F., Yeats, C., Underwood, A., Molloy, A., Connor, D., Shane, H. M., Ashton, P. M., Holden, M. T. G., Grundmann, H., Feil, E. J., Sia, S. B., Donado-Godoy, P., Lingegowda, R. K., Okeke, I. N., Argimón, S. & Aanensen, D. M. & 1 others, NIHR Global Health Research Unit on Genomics and enabling data for the Surveillance of AMR, 25 Nov 2025, In: PLOS Global Public Health. 5, 11, p. 1-14 14 p., e0005256.

    Research output: Contribution to journal › Article › peer-review