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Queen’s DTP: Functional metagenomics for identification of novel antimicrobial resistance genes in environmental viromes


School of Pharmacy

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Dr T Skvortsov , Prof B Gilmore No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Belfast United Kingdom Microbiology Pharmacy

About the Project

This project opportunity is offered as part of the Queen's Doctoral Training Programme - Multi-dimensional approaches to understanding microbe/host interactions in the context of disease, therapeutics and community resilience. For more information, please visit: https://www.findaphd.com/phds/program/queen-s-doctoral-training-programme-multi-dimensional-approaches-to-understanding-microbe-host-interactions-in-the-context-of-disease-therapeutics-and-community-resilience/?p4840

Viruses are the most numerous and most diverse form of life on Earth, present in virtually all environments. The majority of viruses are bacterial viruses, or bacteriophages. Bacteriophages can transfer genes between bacteria, including virulence factors, metabolic genes, and antibiotic resistance determinants. The extent and relevance of antibiotic resistance transmission by bacteriophages is still poorly understood. While antibiotic resistance genes are routinely detected in various viromes, the overall antimicrobial resistance potential of environmental phages remains a controversial topic. As antimicrobial resistance continues to spread, improved understanding of the potential role of bacteriophages as vectors of antibiotic resistance genes is necessary, especially taking into account that DNA fragments inside viral particles are better protected from degradation and can accumulate in the environments over time. To address this, in this study we for the first time will explore the antibiotic resistance potential of viromes by cloning environmental bacteriophage DNA into a broad host range vector, transforming the resulting plasmid libraries into a selection of Gram-positive and Gram-negative bacteria and testing the resulting transformants against a representative selection of antibiotics of different classes for acquisition of antibiotic-resistant phenotypes. The viromes from which antibiotics resistance genes originated will be subjected to next-generation sequencing to investigate what phages the genes came from and their relative abundance in the viromes. The global distribution of these genes will be explored by searching publicly available viral metagenomes. This study will be an exciting opportunity to gain much-needed insight into reservoir of viral genetic diversity and catalogue and characterise functionally active virome-associated antimicrobial resistance genes. This work will be particularly timely and important in light of growing interest to application of bacteriophages against pathogenic bacteria as therapeutic agents.

Applicants should have a 1st or 2.1 honours degree (or equivalent) in a relevant subject. Relevant subjects include Computer Science, Bioinformatics, Molecular Biology, Molecular Microbiology, Virology, Pharmacy, Pharmaceutical Sciences, Biochemistry, Biological/Biomedical Sciences, Chemistry, Engineering, or a closely related discipline. Students who have a 2.2 honours degree and a Master’s degree may also be considered, but the School reserves the right to shortlist for interview only those applicants who have demonstrated high academic attainment to date.

Start Date: October 2021, Duration: 3.5 years

Applicants must submit an online application through the Queen’s Direct Applications Portal: https://dap.qub.ac.uk/portal/user/u_login.php


Funding Notes

There are a number of competition based studentships available, funded by the Department for the Economy (DfE). These opportunities are primarily available for UK applicants but there will be a small number of awards available for EU/international candidates.

References

1. Olena, A. (2016) Phages Carry Antibiotic Resistance Genes. The Scientist
https://www.the-scientist.com/news-opinion/phages-carry-antibiotic-resistance-genes-32389
2. Balcazar JL (2014) Bacteriophages as vehicles for antibiotic resistance genes in the environment. PLOS Pathogens 10(7): e1004219. https://doi.org/10.1371/journal.ppat.1004219
3. Enault F, Briet A, Bouteille L et al. (2017) Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J 11, 237–247.
https://doi.org/10.1038/ismej.2016.90
4. Moon K, Jeon JH, Kang I et al. (2020) Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes. Microbiome 8, 75.
https://doi.org/10.1186/s40168-020-00863-4


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