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 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
Ashley Deventer
Jianbin Zhao
Eva Agnes Laker Odongpiny
Madeleine Clarkson

Selected publications

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
Open access

Etiology and antimicrobial susceptibility patterns of bacteria causing pneumonia among adult patients with signs and symptoms of lower respiratory tract infections during the COVID-19 pandemic in Mwanza, Tanzania: a cross-sectional study
Rukyaa, J., Mushi, M. F., Silago, V., Damiano, P., Keenan, K., Sabiiti, W., Holden, M. T. G., Seni, J. & Mshana, S. E., 5 Sept 2024, In: Pneumonia. 16, 10 p., 16.
Research output: Contribution to journal › Article › peer-review
Open access

Evaluating the public health utility of wastewater-based surveillance of SARS-CoV-2 in Scotland: technical report: a management information release for Scotland
Holden, M., 14 May 2024, Public Health Scotland. 70 p.
Research output: Book/Report › Other report
Open access

Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study
McLachlan, I., Huntley, S., Leslie, K., Bishop, J., Redman, C., Yebra, G., Shaaban, S., Christofidis, N., Lycett, S., Holden, M. T. G., Robertson, D. L., Smith-Palmer, A., Hughes, J. & Nickbakhsh, S., 29 Nov 2024, In: BMJ Open. 14, 11, 15 p., e085332.
Research output: Contribution to journal › Article › peer-review
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, Mmbaga, B. T., Kibiki, G., Stelling, J., Smith, V. A., Sandeman, A., Holden, M. T. G. & HATUA Consortium, 15 Feb 2024, Rochester, NY: SSRN, 26 p.
Research output: Working paper › Preprint
Intersecting social and environmental determinants of multidrug-resistant urinary tract infections in East Africa beyond antibiotic use
HATUA Consortium, 31 Oct 2024, In: Nature Communications. 15, 1, p. 9418
Research output: Contribution to journal › Article › peer-review
Open access

Intersecting social and environmental determinants of multidrug-resistant urinary tract infections in East Africa beyond antibiotic use
Keenan, K. L., Papathomas, M., Mshana, S., Asiimwe, B., Kiiru, J., Lynch, A., Kesby, M., Neema, S., Mwanga, J. R., Mushi, M. F., Jing, W., Green, D. L., Olamijuwon, E. O., Zhang, Q., Sippy, R., Fredricks, K. J., Gillespie, S. H., Sabiiti, W., Bazira, J. & Sloan, D. J. & 8 others, HATUA Consortium, Kibiki, G., Mmbaga, B. T., Aanensen, D., Stelling, J., Smith, V. A., Sandeman, A. & Holden, M., 31 Oct 2024, In: Nature Communications. 15, 11 p., 9418.
Research output: Contribution to journal › Article › peer-review
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
HATUA Consortium, Feb 2024, In: PLOS Global Public Health. 4, 2, e0002709.
Research output: Contribution to journal › Article › peer-review
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
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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