Prof Matt Holden

Prof Matt Holden
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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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Research Overview from research@st-andrews

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).


Recent publications listed in research@st-andrews
25 (of 148 published available) for mtgh (source: University of St Andrews PURE)
Please click title of any item for full details

Antimicrobial resistance in atopic dermatitis Matthew Holden, A.D. Irvine
Annals of Allergy Asthma & Immunology 2019 vol.122 pp.236-240
Chlorhexidine and octenidine use, qac genes carriage, and reduced antiseptic susceptibility in methicillin-resistant Staphylococcus aureus isolates from a healthcare network Htet Lin Htun, Pei Yun Hon, Matthew Holden, Brenda Ang, Angela Chow
Clinical Microbiology and Infection  vol.In press 
Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States Naglaa Mohamed, Yekaterina Timofeyeva, Dorota Jamrozy, Eduardo Rojas, Li Hao, Natalie C. Silmon de Monerri, Julio Hawkins, Guy Singh, Bing Cai, Paul Liberator, Shite Sebastian, Robert G. K. Donald, Ingrid L. Scully, C. Hal Jones, C. Buddy Creech, Isaac Thomsen, Julian Parkhill, Sharon J. Peacock, Kathrin U. Jansen, Matthew Holden, Annaliesa S. Anderson
PLoS ONE 2019 vol.14 
Pseudomonas aeruginosa intensive care unit outbreak Katarina Oravcova, Miguel Pinheiro, Matthew Holden, Gabby Phillips, Jane F. Turton, Stephen Henry Gillespie
Journal of Hospital Infection 2018 vol.98 pp.282-288
An outbreak of Streptococcus pyogenes in a mental health facility Sarah M Bergin, Balamurugan Periaswamy, Timothy Barkham, Hong Choon Chua, Yee Ming Mok, Daniel Shuen Sheng Fung, Alex Hsin Chuan Su, Yen Ling Lee, Ming Lai Ivan Chua, Poh Yong Ng, Wei Jia Wendy Soon, Collins Wenhan Chu, Siyun Lucinda Tan, Mary Meehan, Brenda Sze Peng Ang, Yee Sin Leo, Matthew Holden, Partha De, Li Yang Hsu, Swaine L Chen, Paola Florez de Sessions, Kalisvar Marimuthu
Infection Control and Hospital Epidemiology 2018 vol.39 pp.852-860
Comparative sequence analysis of the capsular polysaccharide loci of Actinobacillus pleuropneumoniae serovars 1-18, and development of two multiplex PCRs for comprehensive capsule typing Janine T Bossé, Yanwen Li, Roberto Fernandez Crespo, Sonia Lacouture, Marcelo Gottschalk, Rita Sárközi, László Fodor, Maria Casas Amoribieta, Øystein Angen, Katerina Nedbalcova, Matthew Holden, Duncan J Maskell, Alexander W Tucker, Brendan W Wren, Andrew N Rycroft, Paul R Langford,
Veterinary Microbiology 2018 vol.220 pp.83-89
Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA Li Hao, Matthew Holden, Xin Wang, Lubomira Andrew, Sabine Wellnitz, Fang Hu, Melissa Whaley, Scott Sammons, Kristen Knipe, Mike Frace, Lucy A McNamara, Paul Liberator, Annaliesa S Anderson
Microbial Genomics 2018 vol.4 
Gene exchange drives the ecological success of a multi-host bacterial pathogen Emily J Richardson, Rodrigo Bacigalupe, Ewan M Harrison, Lucy A Weinert, Samantha Lycett, Manouk Vrieling, Kirsty Robb, Paul A Hoskisson, Matthew Holden, Edward J Feil, Gavin K Paterson, Steven Y C Tong, Adebayo Shittu, Willem van Wamel, David M Aanensen, Julian Parkhill, Sharon J Peacock, Jukka Corander, Mark Holmes, J Ross Fitzgerald
Nature Ecology and Evolution  vol.2 pp.1468-1478
Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections Cosmika Goswami, Stephen Fox, Matthew Holden, Martin Connor, Alistair Leanord, Thomas J. Evans
Microbial Genomics 2018 vol.4 
Global scale dissemination of ST93 Sebastiaan J. van Hal, Eike J. Steinig, Patiyan Andersson, Matthew Holden, Simon R. Harris, Graeme R. Nimmo, Deborah A. Williamson, Helen Heffernan, S. R. Ritchie, Angela M. Kearns, Matthew J. Ellington, Elizabeth Dickson, Herminia de Lencastre, Geoffrey W. Coombs, Stephen D. Bentley, Julian Parkhill, Deborah C. Holt, Phillip M. Giffard, Steven Y. C. Tong
Frontiers in Microbiology 2018 vol.9 
Mobile-genetic-element-encoded hypertolerance to copper protects Staphylococcus aureus from killing by host phagocytes Marta Zapotoczna, Gustavo P Riboldi, Ahmed M Moustafa, Elizabeth Dickson, Apurva Narechania, Julie A Morrissey, Paul J Planet, Matthew Holden, Kevin J Waldron, Joan A Geoghegan
mBio 2018 vol.9 
Naturally occurring polymorphisms in the virulence regulator Rsp modulate Staphylococcus aureus survival in blood and antibiotic susceptibility Aishwarya Krishna, Matthew Holden, Sharon J Peacock, Andrew M Edwards, Sivaramesh Wigneshweraraj
Microbiology  vol.Latest Article 
Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis Janine T. Bossé, Yanwen Li, Rita Sárközi, László Fodor, Sonia Lacouture, Marcelo Gottschalk, Maria Casas Amoribieta, Øystein Angen, Katerina Nedbalcova, Matthew Holden, Duncan J. Maskell, Alexander W. Tucker, Brendan W. Wren, Andrew N. Rycroft, Paul R. Langford,
Veterinary Microbiology 2018 vol.217 pp.1-6
The microevolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare Kerry Andrea Pettigrew, Katarina Oravcova, June Gardner, R. M. Ross Hearn, Debbie Rice, Alison E Mather, Julian Parkhill, Sara J. Brown, Charlotte M. Proby, Matthew Holden
Journal of Investigative Dermatology 2018 vol.138 pp.336-343
The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from Atopic Dermatitis patients M. A. McAleer, D. Bennett, O. M. Fleury, Kerry Andrea Pettigrew, Katarina Oravcova, J. Parkhill, C. M. Proby, R. S. Dawe, J. A. Geoghegan, A. D. Irvine, Matthew Holden
British Journal of Dermatology  vol.Early View 
2015 epidemic of severe Streptococcus agalactiae sequence type 283 infections in Singapore associated with the consumption of raw freshwater fish Shirin Kalimuddin, Swaine L Chen, Cindy T K Lim, Tse Hsien Koh, Thean-Yen Tan, Michelle Kam, Christopher W Wong, Kurosh S Mehershahi, Man Ling Chau, Lee Ching Ng, Wen Ying Tang, Hishamuddin Badaruddin, Jeanette Teo, Anucha Apisarnthanarak, Nuntra Suwantarat, Margaret Ip, Matthew Holden, Li-Yang Hsu, Timothy Barkham,
Clinical Infectious Diseases 2017 vol.64 pp.S145-S152
Diversity of Streptococcus equi subsp. zooepidemicus strains isolated from the Spanish sheep and goat population and the identification, function and prevalence of a novel arbutin utilisation system Karen F Steward, Carl Robinson, Matthew Holden, Simon R Harris, Ana Fernández Ros, Gema Chacón Pérez, Rafael Baselga, Andrew S Waller
Veterinary Microbiology 2017 vol.207 pp.231-238
Enhanced nasopharyngeal infection and shedding associated with an epidemic lineage of emm3 group A Streptococcus Baharak Afshar, Claire E Turner, Theresa Lamagni, Ken Smith, Ali Al-Shahib, Anthony Underwood, Matthew Holden, Androulla Efstratiou, Shiranee Sriskandan
Virulence 2017 vol.8 pp.1390-1400
Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system M Guillermina Casabona, Grant Buchanan, Martin Zoltner, Matthew Holden, Tracy Palmer
Microbiology 2017 vol.163 pp.1851-1863
Genomic dissection of an Icelandic epidemic of respiratory disease in horses and associated zoonotic cases Sigríður Björnsdóttir, Simon R Harris, Vilhjálmur Svansson, Eggert Gunnarsson, Ólöf G Sigurðardóttir, Kristina Gammeljord, Karen F Steward, J Richard Newton, Carl Robinson, Amelia R L Charbonneau, Julian Parkhill, Matthew Holden, Andrew S Waller
mBio 2017 vol.8 
Genomic investigation unmasks evidence of transmission across mycobacterium abscessus cystic fibrosis patients Clare Peters, Devesh Janardan Dhasmana, Kerry Andrea Pettigrew, Ramon Fallon, A-l Seagar, Derek James Sloan, If Laurenson, Matthew Holden, Stephen Henry Gillespie
Thorax 2017 vol.72 pp.A56-A56
Global and regional dissemination and evolution of Burkholderia pseudomallei Claire Chewapreecha, Matthew Holden, Minna Vehkala, Niko Välimäki, Zhirong Yang, Simon R Harris, Alison E Mather, Apichai Tuanyok, Birgit De Smet, Simon Le Hello, Chantal Bizet, Mark Mayo, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Rattanaphone Phetsouvanh, Brian G Spratt, Jukka Corander, Paul Keim, Gordon Dougan, David A B Dance, Bart J Currie, Julian Parkhill, Sharon J. Peacock
Nature Microbiology 2017 vol.2 
Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390 M Guillermina Casabona, Holger Kneuper, Martin Zoltner, Erik Hjerde, Matthew Holden, Tracy Palmer
Microbiology 2017 vol.163 pp.1839-1850
MRSA transmission dynamics among interconnected acute, intermediate-term, and long-term healthcare facilities in Singapore Angela Chow, Vanessa W Lim, Ateeb Khan, Kerry Andrea Pettigrew, David C B Lye, Kala Kanagasabai, Kelvin Phua, Prabha Krishnan, Brenda Ang, Kalisvar Marimuthu, Pei-Yun Hon, Jocelyn Koh, Ian Leong, Julian Parkhill, Li-Yang Hsu, Matthew Holden
Clinical Infectious Diseases 2017 vol.64 pp.S76-S81
Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D Bentley, Angela M Kearns, Matthew Holden
Genome Biology 2017 vol.18