I use genomics to understand the biology and evolution of disease-causing respiratory viruses and bacteria, and how they interact with humans and other microbes. I seek to catalyse the development of new approaches to tackle global public health challenges and enhance pandemic preparedness by generating genomic data at scale, and sharing it openly with the global research community.
Biography
I was fascinated with microbes from a young age, but my passion for investigating infectious diseases was truly ignited when I read Paul de Krieff’s classic book ‘Microbe Hunters’ during my undergraduate studies. The more I read about the origins of HIV, Ebola and Marburg, about bacterial pathogens and antibiotic resistance, the more I wanted to know.
I initially started out working for the Health Protection Agency (now the UK Health Security Agency), testing vaccine candidates to protect against the bacteria that cause meningitis. But it quickly became apparent that I wanted to develop a deeper understanding of the biological phenomena that we were seeing in the lab and so I became a PhD student at the University of Leicester. There I used genomics to understand the mechanisms underpinning evolution and pathogenesis of Pseudomonas aeruginosa, with a particular focus on genomics. I then worked as a postdoctoral fellow at the University of Cambridge employing genomics to track methicillin-resistant Staphylococcus aureus transmission between humans and animals, and then in hospitals and the community. As part of this work, I also used genomics understand how Staphylococcus aureus develops antimicrobial resistance and to uncover novel susceptibilities.
In 2018, I joined the Wellcome Sanger Institute as part of the Health Data Research UK (HDR-UK) substantive site on a UKRI Fellowship to investigate the biological basis of persistent nasal colonisation by S. aureus, a complex and long-standing problem. This required me to take a multidisciplinary approach combining sampling large cohorts of blood donors using microbiology, electronic health data, host genetics and microbiome studies.
In all my studies I have been keen to ensure that my academic research delivers actionable insights for public health, and that the discoveries made from large-scale in silico data lead to hypotheses that can then be investigated in the laboratory. These approaches proved particularly valuable when I became part of the leadership team, and ultimately the Deputy Director, for COG-UK. The consortium brought together academics, public health agencies and clinical partners to deliver genomic surveillance for SARS-CoV-2 on a previously unimaginable scale. My experiences in this pioneering endeavour reinforced the value of collaboration across range of specialisms (experimental, computational, clinical or theoretical) to develop and deliver new science. For this reason, the Respiratory Virus and Microbiome Initiative has collaboration and networking built into its core.
Research
As a microbiologist, I study the intersections between viruses, bacteria and humans, and how they impact on health and disease. My experience helping to coordinate the DNA sequencing, analysis and surveillance of the COVID-19 pandemic in UK has shown me that we can harness the power of large-scale genomics to provide actionable insights to benefit public health. The work of the Sanger Institute, in partnership with the COVID-19 Genomics UK (COG-UK) consortium, has greatly advanced our understanding of viral biology and evolution. The Respiratory Virus and Microbiome Initiative that I lead will build on this to develop tools for future surveillance efforts.
My aim is to accelerate research into respiratory viruses, their interactions with the respiratory microbiome and human host, and to inform the development of new diagnostics and treatments. I seek to achieve this by developing both targeted and pathogen-agnostic genomic tools with which to study viruses and bacteria that commonly infect the respiratory tract at scale.
Taking a multidisciplinary approach is central to fulfilling these aims, and I work closely with a range of collaborators to integrate large-scale viral and microbiome genomic data, human genetics, epidemiological data and clinical cohort data. Our goal is to explore and demonstrate the value in large scale genomic surveillance to clinicians, policy makers, funders, and, ultimately, to the general public.
Publications
Teaching and Supervisions
2023/2024:
- Working with Bacterial Genomes - Training Lead
