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Self-funded BMS project: The ecology, evolution and treatment of polymicrobial cystic fibrosis lung infections


   York Biomedical Research Institute

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  Dr V Friman  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

The global use and misuse of antibiotics has led to the evolution and spread of bacterial resistance to all routinely used antibiotics. At the same time, accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. As a result, while we require new approaches to tackle antibiotic resistant infections, a better understanding of the efficacy of antibiotics in polymicrobial communities is also required. This project will focus on developing phage therapy against Pseudomonas aeruginosa focal bacterial pathogen embedded in polymicrobial, Cystic Fibrosis (CF) lung model bacterial communities. In our previous work (further reading below), we have shown that both the focal pathogen densities and evolutionary trajectories are affected by phage, the presence of competing bacteria and antibiotics treatments. In this project, contribution of each factor will be systematically studied using synthetic Cystic Fibrosis media and clinically relevant bacterial communities derived from CF patients (collaborators in Copenhagen Rigshospitalet). Employed techniques include microbiology, experimental evolution, genome and amplicon sequencing, bioinformatics and ecological and evolutionary theory. Key questions include does the presence of competitors affect the 1) efficacy of antibiotic and phage treatments and/or 2) evolution of phage and antibiotic resistance in P. aeruginosa.

The York Biomedical Research Institute at the University of York is committed to recruiting extraordinary future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with backgrounds in any biological, chemical, and/or physical science, or students with mathematical backgrounds who are interested in using their skills in addressing biological questions. 

Programme: PhD in Biomedical Science (3 years)

Start Date: 1st October 2022 (the student will be affiliated with the Department of Biology)


Funding Notes

This is a self-funded PhD research project. Applicants need to have adequate funds to meet the costs of fees and living expenses for the duration of the PhD programme.

References

Ecology and evolution of antimicrobial resistance in bacterial communities. ISME J (2020),
https://doi.org/10.1038/s41396-020-00832-7
Cross-resistance is modular in bacteria–phage interactions. PLoS Biology (2018),
https://doi.org/10.1371/journal.pbio.2006057
Rapid evolution of generalized resistance mechanisms can constrain the efficacy of phage–antibiotic treatments. Evolutionary Applications (2018),
https://doi.org/10.1111/eva.12653
Bacterial competition and quorum‐sensing signalling shape the eco‐evolutionary outcomes of model in vitro phage therapy. Evolutionary Applications (2017),
https://doi.org/10.1111/eva.12435
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