An interview with Dr Jessica Hedge

Dr Jessica Hedge is a Postdoctoral Researcher in Microbial Genomics at the University of Oxford. Here Jessica talks about the  research she has worked on and how it has helped tackle antimicrobial resistance (AMR), her aspirations for the future and how her career as a research scientist has helped her along this path.

© University of Oxford

Tell us about the AMR research you have worked on?

My research focuses on identifying the bacterial genetic basis of AMR using genome sequence analysis of clinical bacterial strains. My first experience of AMR research was working within the Modernising Medical Microbiology (MMM) Group in Oxford. MMM aims to integrate genome sequence analysis of pathogens into routine clinical diagnostics to speed up identification of AMR infections; for example, AMR diagnosis in Mycobacterium tuberculosis (TB) can take up to 6 weeks using traditional resistance testing, but genome sequencing of the bacterium can reduce this to a matter of hours.

I carried out an evolutionary analysis of over 3500 TB genomes to identify novel genetic variants causing AMR. Since AMR-causing mutations are under positive selection, they are likely to appear multiple times over the evolutionary history of these samples. While these positively-selected mutations didn’t account for any unexplained AMR infections, we found that AMR-associated genes are indeed much more likely to contain mutations that emerge multiple times than genes not associated with AMR.

More recently, I’ve been conducting a bacterial genome-wide association study (GWAS) to try to identify bacterial genetic variants that predispose some strains of Staphylococcus aureus to evolving AMR more often than others. For this project, I work very closely with wet-lab microbiologists who have carried out high-throughput evolution experiments of over 250 S. aureus strains from patients in the UK. If we’re able to identify specific bacterial genes or mutations that make some strains much more likely to evolve AMR, it might be possible to change treatment choices for drug-susceptible infections to prevent the emergence of new AMR infections.

How did this research help to tackle antimicrobial resistance?

Both research projects aim to utilize information contained within bacterial genome sequences to characterise the clinical phenotype of the infection and inform future treatment options for the patient. For example, by speeding up the detection of AMR resistance in TB, clinicians can quickly treat the patient with a drug to which the bacteria are susceptible, thereby reducing any onward spread of the AMR infection. Likewise, if a clinician detects bacterial genetic variants known to increase the probability of AMR evolving to a particular drug, they may be able to prescribe an alternative drug and prevent AMR from evolving within that patient.

Why did you choose to become a microbiologist?

The fact you can see microbes evolving in real-time, before your very eyes! During my undergraduate degree at the University of Manchester, my lecturer Prof. David Robertson, showed an evolutionary tree estimated from HIV gene sequences from a single person – the amount of viral genetic diversity within this single host was enormous, allowing you to see exactly when the AMR mutation arose.  That’s when I decided I wanted to give this a go myself.

Tell us about your biggest professional achievements so far?

In 2014, I became involved in a large, interdisciplinary investigation into a nationwide outbreak of the bacterium Mycobacterium chimaera, led by Public Health England. Very little was know about M. chimaera at the time but it suddenly hit the headlines due to being implicated as the cause of several deaths of patients who had undergone open-heart surgery, sometimes several years previously. By reconstructing the evolutionary history of the strains from both open-heart surgery patients and people who had never had open-heart surgery, we were able to provide evidence supporting a point-source outbreak due to contamination of a piece of equipment used during open-heart surgery.

Outside of my research, I was also particularly proud to represent the Microbiology Society at Parliamentary Links Day 2018. Having developed a strong interest in science policy during my postdoc positions, I was excited to hear from some of the most prominent leaders in UK science policy during the event, which focussed on “Science and the Industrial Strategy”. It was also a fantastic opportunity to meet other society members and guests from the Parliamentary Office of Science and Technology over a lunch at the House of Lords afterwards.

What are your aspirations for the future and how has your career as a research scientist helped you along this path?

Having spent 5 years working in academic research, I’m now keen to bring this experience to a position outside of academia to develop new skills and perhaps interact more directly with both industry and government. My academic training has provided me with a broad set of skills in critical thinking, problem solving, quantitative data analysis, data visualisation, synthesis of complex information, oral and written communication for a variety of different audiences, and project management. Alongside my research, I’ve spent the last year leading the development of a website showcasing the range of careers people go into after completing a PhD (, which has highlighted to me how valuable each of these skills can be for roles in other sectors.

Why do you think the Microbiology Society is important?

The Microbiology Society provides a wealth of opportunities for career development, such as resources to engage the public with your research, convening meetings and conferences for communicating your research to the research community, facilitating member engagement with science policy, and awarding researchers prizes in recognition of their achievements. This is particularly important for early career researchers like myself, who may want to either develop skills and explore options for careers beyond academia, or forge new collaborations outside of their current institution for the development of fellowship applications. Either way, the society has an important role in allowing researchers to obtain a broader understanding of where their research fits into the bigger picture, both academically and within society more generally.

Personally, the Society has provided me with numerous opportunities to learn more about careers beyond academia and meet people working within different organisations. For example, when I participated in their workshop to develop their new  “Research Environment Position Statement”, I was introduced to several people working in academia, government and funding bodies. Following attendance at Parliamentary Links Day, I was given the opportunity to hone my writing skills by blogging about the experience on MicrobePost, and by registering my interest in policy in the members section of the website, I’ve been able to contribute to the Society’s response to a Parliamentary Inquiry on AMR. Finally, I’ve also benefitted from one of the Society’s bursaries to attend a workshop on “Science Policy: Improving the Uptake of Research into UK Policy” at the Wellcome Genome Campus.

If you are a member of the Society and would like to find out more about how you can get involved with Society activities and/or showcase your research, please email us at [email protected].