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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Recent Publications:

5 (of 156 /dk/atira/pure/researchoutput/status/published available) for mtgh (source: University of St Andrews PURE)
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A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage Stephen Fox, Cosmika Goswami, Matthew Holden, James P. R. Connolly, James Mordue, Nicky O’Boyle, Andrew Roe, Martin Connor, Alistair Leanord, Tom J. Evans
Scientific Reports 2020 vol. 10
Draft genome sequences of the type strains of Actinobacillus indolicus (46K2C) and Actinobacillus porcinus (NM319), two NAD-dependent bacterial species found in the respiratory tract of pigs Janine T Bossé, Yanwen Li, Roberto Fernandez Crespo, Øystein Angen, Matthew Holden, Lucy A Weinert, Duncan J Maskell, Alexander W Tucker, Brendan W Wren, Andrew N Rycroft, Paul R Langford,
Microbiology Resource Announcements 2020 vol. 9
Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli Cosmika Goswami, Stephen Fox, Matthew Holden, Martin Connor, Alistair Leanord, Thomas J. Evans
Microbial Genomics 2020 vol. 6
Antimicrobial resistance in atopic dermatitis Matthew Holden, A.D. Irvine
Annals of Allergy Asthma & Immunology 2019 vol. 122 pp. 236-240
Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics Mark R Davies, Liam McIntyre, Ankur Mutreja, Jake A Lacey, John A Lees, Rebecca J Towers, Sebastián Duchêne, Pierre R Smeesters, Hannah R Frost, David J. Price, Matthew Holden, Sophia David, Philip M Giffard, Kate A Worthing, Anna C Seale, James A Berkley, Simon R Harris, Tania Rivera-Hernandez, Olga Berking, Amanda J Cork, Rosângela S L A Torres, Trevor Lithgow, Richard A Strugnell, Rene Bergmann, Patric Nitsche-Schmitz, Gusharan S Chhatwal, Stephen D Bentley, John D Fraser, Nicole J Moreland, Jonathan R Carapetis, Andrew C Steer, Julian Parkhill, Allan Saul, Deborah A Williamson, Bart J Currie, Steven Y C Tong, Gordon Dougan, Mark J Walker
Nature Genetics 2019 vol. 51 pp. 1035-1043