James Delaney

University of Warwick

Project

Identifying drivers of antibiotic resistance in river systems

Supervisors

Professor Liz Wellington (University of Warwick), Dr Christopher Quince (University of Warwick) and Dr Andrew Singer (NERC CEH Wallingford).

PhD Summary

Until recently, antibiotic resistance was analysed purely as a medical problem, but it is now understood that the environment has a key role to play as a reservoir of antimicrobial resistance genes (AMR). AMR genes located on bacterial plasmids and other horizontally transmitted gene elements can be transported from environmental microorgansisms to harmful pathogens, providing them with resistance. This project will aim to use a combination of newly available metagenome sequence data and bioinformatic techniques to better understand the role played by the environment in AMR. Analysis will be conducted on over a terabase of microbial DNA metagenome sequence samples, all of which have been derived from the Thames River.

What inspires you?

During my undergraduate research project, I studied the impact of metal pollution on antimicrobial resistance in environmental bacterial isolates derived from soils. As a result, I became fascinated by the synergistic and antagonistic effects that environmental factors can have on microbial communities and the implications that this could have for human health. Furthermore, during my summer research internship as part of the “Welsh Crucible” network, I was involved in a project looking at the antimicrobial/ antifungal/ anti-inflammatory potency of a various natural remedies that were initially published by the famous “Physicians of Myddfai” in the 11th century. The ancient remedies had recently been translated by a group of Linguists at the University of Wales and we wanted to investigate whether any of the natural ingredients could be effective in modern medicine. I found this to be a highly enjoyable experience and it expanded my interest in the natural world.

Previous Activity

I studied for a BSc in Medical Genetics and an MSc by research (Microbiology) at Swansea University. My MSc by research project was funded by the Welsh Government’s “Knowledge Economy Skills Scholarship” (KESS) programme, and therefore involved direct collaboration with an industrial partner. During the project, I analysed the efficacy of three currently manufactured products aiding in the removal of bacteriological contamination and/or biofilms for the wet leisure industry. The project also involved assessing the impact that the over/ misuse of chemical products in water systems could have in terms of the spread of antimicrobial resistance (AMR). In addition, I also ran some toxicology studies, in order to ensure that the levels of chemicals used in the production of anti- biofilm products were safe for human exposure.

Why did you choose Docotoral Research?

Throughout my undergraduate and MSc projects, I had been studying the impact of environmental factors upon antimicrobial resistance and biofilm formation within soil/ water settings. However, there were still a number of research questions that I really wanted answers to. Such as: What are the genetic drivers of antibiotic resistance as a result of exposure to different environmental conditions? What role does pollution play in driving antibiotic resistance within river settings specifically? This doctoral project provided a great opportunity for me to continue my research in this area, whilst allowing me to learn a variety of new metagenomic and bioinformatic techniques.

Why did you choose a CENTA Studentship?

I liked the fact that CENTA was a collaboration between 5 excellent universities, all of which possess unique expertise and facilities that are available to students. All of the universities provide individual training courses throughout the PhD programme, which would allow me to enhance my skillset in many areas. Furthermore, CENTA allowed the opportunity to work as part of a larger doctoral cohort alongside many other candidates from different subject areas, which could provide good opportunities for collaboration in the future. Lastly, it was always my intention to obtain an NERC PhD position if possible, as I felt that their generous funding and prestigious reputation would put me in a good position for my future career.

What are your future plans

I feel that studying for a PhD with CENTA and the University of Warwick will be highly valuable, whichever area of work I decide to go into. For example, if I wanted to carry on research to postdoctoral level, which would be my current intention, the research and presentation skills that I will learn during this PhD programme will be essential. The fact that the University of Warwick has an international reputation for microbiology will also help to enhance my profile. However, if I wanted to go into other professional areas, the fact that this DTP programme involves collaboration with the Centre for Ecology and Hydrology at Wallingford will provide me with a number of enhanced research skills that could be applied to industry also. Lastly, the organisational and professional skills that a PhD provides you with, as well as the discipline of working on an extended research project for 3.5 years, will be highly regarded by different employers.