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 23 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
- Jianbin Zhao
- Joanna Rivas
- Eva Agnes Laker Odongpiny
- Sepideh Benvari
- Madeleine Clarkson
- Ashley Deventer
Selected publications
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Open access
Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium
McHugh, M. P., Pettigrew, K. A., Taori, S., Evans, T. J., Leanord, A., Gillespie, S. H., Templeton, K. E. & Holden, M. T. G., Mar 2024, In: Journal of Antimicrobial Chemotherapy. 79, 3, p. 656-668 13 p., dkae023.Research output: Contribution to journal › Article › peer-review
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Open access
Evidencing the intersection of environmental, socioeconomic, behavioural and demographic drivers of antibacterial resistance in East Africa
Keenan, K., Papathomas, M., Mshana, S. E., Asiimwe, B., Kiiru, J., Lynch, A. G., Kesby, M., Neema, S., Mwanga, J. R., Mushi, M. F., Green, D. L., Jing, W., Olamijuwon, E., Zhang, Q., Sippy, R., Fredricks, K. J., Gillespie, S. H., Sabiti, W., Bazira, J., Sloan, D. J., & 7 others , 15 Feb 2024, Rochester, NY: SSRN, 26 p.Research output: Working paper › Preprint
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Open access
Predominance of multidrug-resistant bacteria causing urinary tract infections among symptomatic patients in East Africa: a call for action
Maldonado-Barragán, A., Mshana, S. E., Keenan, K., Ke, X., Gillespie, S. H., Stelling, J., Maina, J., Bazira, J., Muhwezi, I., Mushi, M. F., Green, D. L., Kesby, M., Lynch, A. G., Sabiiti, W., Sloan, D. J., Sandeman, A., Kiiru, J., Asiimwe, B. & Holden, M. T. G., Feb 2024, In: JAC-Antimicrobial Resistance. 6, 1, 11 p., dlae019.Research output: Contribution to journal › Article › peer-review
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Open access
Treatment seeking and antibiotic use for urinary tract infection symptoms in the time of COVID-19 in Tanzania and Uganda
Olamijuwon, E. O., Keenan, K. L., Mushi, M. F., Kansiime, C., Konje, E. T., Kesby, M., Neema, S., Asiimwe, B., Mshana, S. E., Fredricks, K. J., Sunday, B., Bazira, J., Sandeman, A. F., Sloan, D. J., Mwanga, J. R., Sabiiti, W., Holden, M. & CARE Consortium, 19 Jan 2024, (E-pub ahead of print) In: Journal of Global Health. 14, 10 p., 05007.Research output: Contribution to journal › Article › peer-review
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Open access
Treatment seeking behaviours, antibiotic use and relationships to multi-drug resistance: a study of urinary tract infection patients in Kenya, Tanzania and Uganda
Sado, K., Keenan, K., Manataki, A., Kesby, M., Mushi, M. F., Mshana, S. E., Mwanga, J. R., Neema, S., Asiimwe, B., Bazira, J., Kiiru, J., Green, D. L., Ke, X., Maldonado-Barragán, A., Abed Al Ahad, M., Fredricks, K. J., Gillespie, S. H., Sabiiti, W., Mmbaga, B. T., Kibiki, G., & 6 others , 16 Feb 2024, In: PLOS Global Public Health. 4, 2, 20 p., e0002709.Research output: Contribution to journal › Article › peer-review
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Open access
Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus
van Hal, S. J., Jensen, S. O., Tong, S. Y. C., Bentley, S. & Holden, M. T., Apr 2024, In: Journal of Antimicrobial Chemotherapy. 79, 4, p. 891–896Research output: Contribution to journal › Article › peer-review
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Open access
Klebsiella pneumoniae carbapenamases in Escherichia coli isolated from humans and livestock in rural South-Western Uganda
Tuhamize, B., Asiimwe, B., Kassaza, K., Sabiiti, W., Holden, M. & Bazira, J., 13 Jul 2023, In: PLoS One. 18, 7, 10 p., e0288243.Research output: Contribution to journal › Article › peer-review
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Open access
Adeno-associated virus 2 infection in children with non-A-E hepatitis
Ho, A., DIAMONDS consortium, ISARIC4C investigators, Willett, B. J., Breuer, J., Semple, M. G., Turner, D., Baillie, J. K. & Thomson, E. C., 18 May 2023, In: Nature. 617, p. 555-563Research output: Contribution to journal › Article › peer-review
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Open access
Allele distribution and phenotypic resistance to ciprofloxacin and gentamicin among extended spectrum β-lactamases producing Escherichia coli from urine, stool, animals and environments of patients with presumptive urinary tract infection in Tanzania
Mwakyoma, A. A., Kidenya, B. R., Minja, C. A., Mushi, M. F., Sandeman, A. F., Sabiiti, W., Holden, M. & Mshana, S. E., 5 Jun 2023, In: Frontiers in Antibiotics. 2, 11 p., 1164016.Research output: Contribution to journal › Article › peer-review
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Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent
Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N., Fjodorova, L., Forrest, R., Goldstein, E., Gunson, R., Haughney, J., Holden, M. T. G., Honour, P., Hughes, J., James, E., Lewis, T., & 18 others , 1 Aug 2023, In: Journal of Infection. 87, 2, p. 128-135 8 p.Research output: Contribution to journal › Article › peer-review