Prof Matthew Holden
Director of Impact
Professor
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 St Andrews 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
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Open access
Draft genome sequence of a non-tuberculous Mycobacterium strain isolated from a clinical urine sample
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
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Open access
Genome-based source attribution using a One Health Escherichia coli isolate collection from 2013 to 2023 in Scotland
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, , 20 Apr 2026, (E-pub ahead of print) In: Microbial Genomics. 12, 4, 001693.Research output: Contribution to journal › Article › peer-review
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Open access
Risks and possible implications of weight gain after switch to dolutegravir- in a large Ugandan cohort of people living with HIV
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 PrintResearch output: Contribution to journal › Article › peer-review
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Open access
A programmatic assessment of dolutegravir adverse events and discontinuations in Uganda
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
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Open access
Assessing the role of topical vancomycin in reducing surgical site infections following spinal surgery: a comprehensive review
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
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Open access
Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment
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
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Open access
Conference report: The second bacterial genome sequencing Pan-European Network conference
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, , 23 Oct 2025, In: Microbes and Infection. 27, 7, p. 1-8 8 p., 105557.Research output: Contribution to journal › Article › peer-review
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Open access
Integrated population clustering and genomic epidemiology with PopPIPE
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
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Open access
Modelling interventions to combat antibacterial resistance in East Africa using causal Bayesian networks
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, , 4 Feb 2025, Research Square.Research output: Working paper › Preprint
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Open access
Monitoring antimicrobial resistance trends from global genomics data: amr.watch
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, , 25 Nov 2025, In: PLOS Global Public Health. 5, 11, p. 1-14 14 p., e0005256.Research output: Contribution to journal › Article › peer-review