Prof Matt Holden:

Since the first bacterial genome was sequenced in 1995, whole genome sequencing (WGS) has provided unprecedented insights into the genetics and evolution of microbial pathogens. Having worked at the Sanger Institute 13 years on a broad range of bacterial genomes, I recently moved to the School of Medicine establishing a pathogenomics group. Research in my group is directed at two main areas: translational genomics, the application of WGS in clinical microbiology; and experimental genomics, using data WGS to investigate the relationship between pathogens’ genotypes and phenotypes.

The research areas that the group are focused on include: developing rapid WGS to combat hospital-associated infections, the molecular basis of antibiotic resistance and virulence, and epidemiology and evolution of methicillin resistant S. aureus (MRSA).


I started my research career with a PhD at Warwick University, studying the distribution and regulation of cryptic antibiotic genes in environmental and plant pathogenic bacteria. As a postdoc I then spent four years at the University of Nottingham, investigating bacterial communication. Initially working on the role of N-acyl homoserine lactones in quorum sensing in Pseudomonads, and then moving ‘languages’ to investigate peptide autoinducer-dependent regulation of virulence in Staphylococcus aureus. I then joined the The Wellcome Trust Sanger Institute in 2000, and have involved in the analysis of the genomes of a wide range of bacterial pathogens including Yersinia pestis, Salmonella typhi, Streptococcus pyogenes, Burkholderia pseudomallei, Burkholderia cenocepacia and S. aureus. With developments in next generation sequencing, the focus of my work has shifted towards populations studies, investigating genome diversity and pathogen evolution, as well as the application of sequencing in clinical microbiology. In 2013 I moved to the Medical School at University St Andrews to establish a research group focusing on experimental and translational pathogen genomics.

My research interest include: the survival and evolution of MRSA, and probing the link between a pathogen’s genotype and virulence, and also the application of genomics in clinical setting to combat hospital-associated infections.

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source: symbiosis

Recent Publications:

5 (of 169 /dk/atira/pure/researchoutput/status/published available) for mtgh (source: University of St Andrews PURE)
Please click title of any item for full details

Clinical perspectives in integrating whole genome sequencing into the investigation of healthcare and public health outbreaks – hype or help? Stephen Henry Gillespie, Kerry A. Pettigrew, Matthew Holden
Journal of Hospital Infection 2021 vol. 109 pp. 1-9
Dispensing antibiotics without prescription at the community pharmacies and accredited drug dispensing outlets in Tanzania Pendo M. Ndaki, Martha F. Mushi, Joseph R. Mwanga, Eveline T. Konje, Nyanda E. Ntinginya, Blandina T. Mmbaga, Katherine Lisa Keenan, Wilber Sabiiti, Mike Kesby, Manuel Fernando Benitez Paez, Alison Fiona Sandeman, Matthew Holden, Stephen E. Mshana,
Antibiotics 2021 vol. 10
Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments Irene Sarah Fortune, Andrew John Blight, Patricia Browne, Morgan Hartley, Matthew Holden, David Maxwell Paterson
PLoS ONE 2021 vol. 16
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland Ana da Silva Filipe, James G. Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha Jesudason, Natasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A. McAllister, John T. McCrone, Sarah E. McDonald, Martin Patrick McHugh, A. Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B. Sreenu, Elizabeth Wastnedge, Matthew Holden, David L. Robertson
Nature Microbiology 2021 vol. 6 pp. 112-122
Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013-2014 Manuel C Jamoralin, Silvia Argimón, Marietta L Lagrada, Alfred S Villamin, Melissa L Masim, June M Gayeta, Karis D Boehme, Agnettah M Olorosa, Sonia B Sia, Charmian M Hufano, Victoria Cohen, Lara T Hernandez, Benjamin Jeffrey, Khalil Abudahab, John Stelling, Matthew Holden, David M Aanensenb, Celia C Carlosa
Western Pacific Surveillance and Response Journal 2021 vol. 12 pp. 17-25