AMI internship leads Zoe down path of antimicrobial resistance

Zoe Dunphy undertook a lab internship in 2020 in Trinity College Dublin’s microbiology department, funded by an AMI Summer Studentship Grant. She reveals how that experience has developed her work on AMR.

Zoe was first introduced to the idea of a lab-based internship in the third year of her undergraduate degree as something that would be advantageous, not only for gaining experience but also for professional development going forward. 

“I knew immediately that this was something I was interested in, as I had always enjoyed our practical classes and was eager to learn more about research practice,” she says. 

“I got in contact with Dr Marta Martins from the Microbiology Department at Trinity College Dublin where I was a student to discuss the possibility of such an internship and she suggested the AMI Student Placement Scholarship. 

“We submitted a project proposal investigating the relationship between antibiotic and biocide cross-resistance in bacterium Klebsiella pneumoniae and also its biofilm formation as linked to this resistance. We were successful in our application in 2020 but due to the COVID-19 pandemic my internship took place in Dr. Martins’ lab in the summer of 2021.”

Invaluable experience

During this internship, Zoe says she gained invaluable experience working with antibiotic resistant bacteria, from safety and handling practices to common techniques investigating the features of antibiotic resistant bacteria, such as permeability assays, antibiotic susceptibility profiling, biofilm quantification assays and phenotypic tests. 

All of these taught her the importance of organisation and planning as much as the skills and techniques themselves. 

“I gained confidence in my abilities in these laboratory practices, even optimising some of my experiments to ensure consistent results. We found that several of the K. pneumoniae clinical isolates we investigated, all of which had multidrug-resistant profiles, exhibited high levels of cell permeability, likely owing to their efflux capabilities which are often overexpressed in MDR strains,” Zoe says. 

“In addition to permeability, several of these clinical isolates were good biofilm formers, with biofilm biomass increasing upon addition of biocides such as hydrogen peroxide and ethanol, even up to two times the minimum bactericidal concentration. This indicates that biofilm formation underpins biocide tolerance and even possibly antibiotic cross-resistance in these clinical isolates of K. pneumoniae.

“This internship has only increased my interest in laboratory-based research now that I have had a chance to carry out my own experiments and link the resulting data together in a meaningful way which has allowed me to link different concepts together in a real-time setting which I would have learned from my undergraduate degree. It has only left me excited to answer more questions arising from these findings.”

Career path

Now in the second year of a PhD in antimicrobial resistance, Zoe is working in the same lab where she carried out her AMI internship, under supervisor Dr Marta Martins. Her PhD is funded by Irish Research Council Enterprise Partnership Scholarship 2020.

“The internship really helped with securing the PhD, I believe, as it gave me not only lab experience but also experience in writing grant applications and helped me decide if I wanted to go into research,” Zoe says.

“My project is in the area of antimicrobial resistance and hospital-acquired infections which I believe are very interconnected, and my aim is to develop a method for sampling and analysing the microbiome contained on Personal Protective Equipment derived from hospitals in Ireland, using a genomics approach and phenotypic testing/AST testing of recovered bacterial samples.”

Since completing the internship she has attended a major conference, ECCMID 2022, as well as other focus meetings within the area of microbiological research.

“AMR is an urgent global issue which requires increased attention and funding in order to make any improvement,” Zoe says.

“Multidrug resistant infections are a major cause of death and can be disseminated worldwide due to the spread and transfer of genes encoding resistance, leaving physicians with a rapidly decreasing list of antibiotics to treat their patients with.

“I intend to remain in the area of AMR as I am still very passionate about this research and would hope to contribute to the fight against antibiotic resistance in anyway I can.”