Bringing pathogen genome sequencing to clinical settings

Earlier in Michaelmas term Dr Bernadette Young joined Oriel College as Fellow and Tutor in Clinical Medicine. She succeeds Professor Christopher Conlon, now an Emeritus Fellow, who held the position from 2005 until his retirement earlier this year.

Going against the migration of medics to Australia, Young completed her undergraduate studies at the University of Melbourne before moving to Oxford to continue her clinical and academic training and to work.

She completed a series of academic rotations at the Thames Valley deanery, working on clinical trials for infection treatments and also learning techniques in molecular epidemiology. Then came 2013 and she was awarded a Wellcome Trust Research Training Fellowship to conduct a DPhil in Clinical Medicine at Wolfson College, Oxford.

During her DPhil Young was based at the Nuffield Department of Medicine, working with the Modernising Medicine Microbiology group and researching genetic factors determining the virulence of Staphylococcus aureus bacteria.

Most strains of S. aureus bacteria act as commensal members of the natural human microbiome, causing neither benefit nor harm. But some can lead to infections that are transmissible from one person to another.

Young’s research saw her look for associations between the virulence of strains and their genomes. Understanding the genetic basis of bacterial virulence in this way opens the door to preventing infection through developing vaccines, she said.

Among her findings is a single bacterial toxin which is critical to the development of pyomyositis, a soft tissue infection resulting in an abscess.

Young explained that a hope shared by many doctors is that pathogen genome sequencing will deliver benefits directly to patients. “This will require us to translate sequencing from being a research tool, or the province of specialist reference laboratories, and into the routine clinical laboratory,” she added.

Introducing genome sequencing to clinical settings would allow doctors to offer same-day diagnoses of infections and to gauge their virulence and also the presence of antibiotic resistance.

Alongside her new role at Oriel College, Young is a Consultant in Infection at Oxford University Hospitals NHS Foundation Trust. She is also now an Honorary Researcher at the Nuffield Department of Medicine.

During the Covid-19 pandemic, surveillance of variants was done at Oxford University Hospitals using state-of-the-art tools and techniques.

Meanwhile, at the Nuffield Department of Medicine, Young conducted research to help guide public health policy.

She and her colleagues compared the policy that all students identified as contacts should isolate for ten days with the alternative that students should test daily for Covid-19 using lateral flow tests, isolating only when testing positive for the virus.

Finding that there was no evidence of a higher infection rate in schools when using lateral flow tests to release students from isolation, and that the number of contacts who went on to test positive for Covid-19 was only around two per cent, they concluded that implementing the alternative policy was a safe way to minimise disruption to education while controlling the spread of the virus.

Currently, at Oxford University Hospitals’ Bone Infection Unit, Young is looking to improve diagnoses and treatments of bone and joint infections.

The Bone Infection Unit is a national specialist unit dedicated to researching and treating all aspects of bone or joint infections, and the bacteria that cause bone or joint infections exhibit considerable variability, with the infections that result from some being especially challenging to treat.

Young is interested in understanding what traits certain strains of bacteria have that makes them “sticky” and intractable with the aim of informing the development of new treatments.