HOLDEN RESEARCH GROUPResearch at the University of St Andrews School of Medicine
Matthew Holden – Group Leader
I started my research career with a PhD at Warwick University supervised by Prof. George Salmond, 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 in Prof Gordon Stewart’s and Prof. Paul William’s labs investigating and quorum sensing bacterial communication. In 2000 I joined the Pathogen Sequencing Unit at the The Wellcome Trust Sanger Institute and where I worked on the annotation and analysis of the genomes of a wide range of bacterial pathogens. As a result of developments in sequencing technology, 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 University of St Andrews in Scotland to establish a research group focusing on experimental and translational genomics.
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Current Group Members
Dr Catriona Harkins PhD Student
Clinical PhD student at the University of Dundee
In 2007 I graduated from the University of Glasgow Medical School with Commendation. After completing general medical training I began to specialize in Dermatology. I subsequently moved to the University of Dundee as a clinical lecturer in Dermatology in 2012. As a dermatologist I am interested in the role microbes play in the aetiology of skin disease, ranging from the infectious to the inflammatory.
I have a particular interest Staphylococcus aureus and its involvement in the common skin disease atopic eczema (AE). Colonisation with S. aureus is well recognised in atopic eczema, and there is a clinically observable link between S. aureus burden and disease flares. This highly adaptable human pathogen has an arsenal of virulence, adhesive and adaptive mechanisms to survive the host environment. To date, only a selection of candidate genes within this organism have been interrogated with respect to their contribution to inflammatory skin disorders, such as AE. By utilising a whole genome approach I aim to assess the genetic diversity and characteristics of S. aureus populations isolated from patients with eczema.
Martin McHugh PhD Student
I gained a BSc in Biological Sciences from the University of Edinburgh with Honours in Infectious Diseases in 2010. I then took up a post as a Trainee Clinical Scientist at the Mycology Reference Centre Manchester. During my training I was seconded to other NHS diagnostic labs within Manchester and further afield, gaining training in the diagnosis and management of bacterial, viral, fungal and parasitic infections. During this time, I also gained an MSc in Medical Microbiology from the University of Manchester, with distinction. My MSc dissertation looked at the transcriptional response of Candida albicans biofilms when exposed to the antifungal drug fluconazole.
In 2014 I took up a post at the Royal Infirmary of Edinburgh as an Associate Clinical Scientist. My role is to develop the laboratory diagnostic service and I have been involved in a number of projects evaluating methods for the detection of bacterial and viral pathogens, mainly using PCR-based assays. Also in 2014 I gained registration as a Clinical Scientist with the Health and Care Professions Council and in early 2015 I passed the Part 1 examination in microbiology for Fellowship of the Royal College of Pathologists. I am interested in using modern techniques to improve the diagnosis of hospital-associated and antimicrobial-resistant infections, with an aim to allow better clinical management of these conditions and improve patient outcomes.
I started PhD study at the University of St Andrews in 2015, under the supervision of Dr Matthew Holden. As part of the SHAIPI consortium I will be looking into the genomic epidemiology of vancomycin-resistant enterococci (VRE) in Scotland. VRE is an increasing concern in immunocompromised patients and local outbreaks have been seen in high-risk settings. Increased understanding of these organisms may allow targeted interventions to decrease VRE spread and acquisition within healthcare settings.
Dr Katarina Oravcova Research Fellow
As postdoctoral research fellow in Dr. Matt Holden’s group in the Medical School of University of St Andrews, my main research interests focus on the investigation of HAI (hospital associated infections) outbreaks involving near real-time WGS and bioinformatics analysis. Having worked for over four years with Professor Stephen Gillespie, also at the USTAN Medical School, my research has focused identification of phenotypic and genotypic biomarkers of Mycobacterium tuberculosis dormancy; in particular, the involvement of lipid bodies in dormancy and drug response, and application of experimental data in predictive models. My additional research involves the investigation of antibiotic resistance acquisition and transfer in relation to biological fitness of mutant bacteria.
Molecular- and WGS-based approaches are powerful tools in the discovery of novel species and characterization of their virulence traits. I am interested in applying these in the elucidation of pathogenic or opportunistic nature of a recently described bacterium Mycoplasma amphoriforme.
I graduated and subsequently gained a Master’s degree in Chemistry and Biotechnology. I obtained my PhD degree in Molecular Biology from the Comenius University in Bratislava, Slovakia in 2009 with the thesis on the identification and genotyping of a foodborne pathogen Listeria monocytogenes. My working experience in the Food Research Institute, Bratislava and the ITACyL, Valladolid, Spain led to the development of numerous assays for genotypic and phenotypic characterization of foodborne and veterinary pathogens with the aim to elucidate their phylogenetic relationships and persistence in the environment.
Dr Kerry Andrea Pettigrew Research Fellow
Research: Genetic epidemiology, cognitive traits, molecular biology, translational genomics
After completing my PhD in Genetic Epidemiology in the Nephrology Research Group at Queens University Belfast, I have spent my postdoctoral career in both academic research and genotyping service environments. I have applied genotyping, sequencing and statistical analysis techniques to a range of medical research areas, including cancer, cardiovascular disease and cognitive development. In April 2015, I joined the Holden group to perform next-generation sequencing on bacterial isolates derived from hospital-associated infection as part of the SHAIPI consortium.