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Nationwide analysis of Antimicrobial Resistance in soil environments to bridge the current data knowledge gaps

   Department of Biology

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  Prof Fiona Walsh  No more applications being accepted  Funded PhD Project (European/UK Students Only)

About the Project

PhD (EPA): Funded 4-year PhD studentship:

“Nationwide analysis of Antimicrobial Resistance in soil environments to bridge the current data knowledge gaps”

The overall concept underpinning the project is to take the current opportunity provided by the nationwide Farm Environmental Study Programme conducted by the Department of Agriculture, Food and the Marine (DAFM) to study a very large and widely distributed collection of soils for their antimicrobial resistance (AMR) profiles and to use a subset of these to correlate with microbial biodiversity. This will provide the largest and most comprehensive national study of soils and their AMR composition globally. The main idea is simple: analyse as many soil samples as possible for AMR genes and their relative abundances and correlate these data with the array of soil characteristics collected by DAFM and the microbial biodiversity of a subset. This project will analyse the genomes of ESBL Escherichia colicollected as part of the soil survey and compare them with those available in online databases. This will also be a large resource of environmentally isolated ESBL E. coli and their genomic data for other researchers or interested parties.

PhD techniques:

DNA extraction from soil, high-throughput generation of the Loop-mediated isothermal amplification (LAMP) assay analysis of AMR genes, qPCR analysis of AMR gene relative abundances, bacterial biodiversity analysis using microbiome analysis, whole genome sequencing and data analysis of E. coli genomes. Data analysis of the combined data generated. Communication of the findings with stakeholders. 

The ideal candidate:

I am looking for a highly motivated individual with a strong background and interest in any of the following areas: microbiology, molecular biology, genomics, microbiomes. The ideal candidate should be able to work independently, but yet enjoy working in a team. Applicants must hold a BSc or MSc. 

The research group of Prof Walsh is located in the Department of Biology, Maynooth University, Ireland, EU ( This group focuses on antimicrobial resistance (AMR) in bacteria, with a specific interest in plasmid mediated resistance and its transfer between bacteria and biomes. We use culture and -omics techniques to investigate AMR from a One Health perspective.  

The start date for the PhD position is January 2023. The tax-free salary is €18,500 per year, university fees are paid by the project. Please send a detailed CV and contact details of two references to [Email Address Removed] before November 30th 2022

Funding Notes

Funding to the level of EU fees is available.
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