PhD Student Vacancy: EastBio – Antimicrobial resistance (AMR): from agricultural environment to food chain

Job title:

PhD Student Vacancy: EastBio – Antimicrobial resistance (AMR): from agricultural environment to food chain

Company

The James Hutton Institute

Job description

Background:Three key transmission routes of AMR in the agricultural environment are faecally-derived fertilisers, irrigation water and surface water (Koutsoumanis et al., 2021). A pre-requisite for generating reliable data on agricultural matrices is the development and application of appropriate detection methods and downstream analyses. Although studies have reported the presence of AMR in rivers, sediments and soil (e.g. Pagaling et al., 2023), there is an urgent need to harmonise AMR surveillance to avoid global inconsistency of methods to further develop the ‘One Health’ approach.At present, methods to detect AMR in soils, waters and organic wastes include molecular approaches such as high throughput q-PCR or metagenomics and culture-based techniques where organisms are isolated and then subsequently tested for antimicrobial susceptibility. All generate different levels of data complexity and ease of linkage to risk to human health; however there is no clear consensus on measuring AMR in the environment.Aim:To apply and evaluate methods to determine AMR in the agricultural environment, to address knowledge gaps about its role in the transmission of AMR to the food chainApproach:The student will review and select methods to compare for detecting AMR in the agricultural environment, including high throughput q-PCR, metagenomics, and the tricycle approach (WHO, 2021) for ESBL E. coli isolates. They will be trained in DNA extraction, HT-q-PCR, and culture/susceptibility testing.Spatio-temporal sampling campaigns will be devised to test the hypothesis that AMR enters the food chain (livestock or crops) via faecally-derived materials entering the farm environment. Laboratory microcosm experiments will supplement these to test the effects of specific environmental conditions on the suitability of different methods to determine AMR. Background physico-chemical analyses of environmental matrices will provide contextual understanding.Statistical analyses will evaluate relationships between methods and to assess how they reflect AMR variability in the farm environment.The student will work with supervisors and advisors from various disciplines, learning techniques in microbiology/molecular biology, bioinformatics, statistics and environmental chemistry. Welcomed into the vibrant graduate schools at the James Hutton Institute and Strathclyde University, the student will have the opportunity to engage with stakeholders and policymakers and academics in knowledge exchange activities, facilitating strong routes to impact in this forefront area of research.The EastBio partnership offers fully-funded competition based studentships. Funding covers Home (UK fees), a stipend at UKRI norm level (£19,327 for 2024/2025) and project costs. Application guidance can be found on the Eastbio website; . Information on UKRI-BBSRC can be found on the UKRI websiteWe will not consider the use of 3rd party recruitment agencies for the sourcing of candidates for this position.The James Hutton Institute is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.The James Hutton Institute is a: Stonewall Diversity Champion; Athena SWAN Bronze Status Holder; Disability Confident Committed Employer and a Living Wage Employer.The James Hutton Institute is Happy to Talk Flexible Working.

Expected salary

£19237 per year

Location

Dundee

Job date

Wed, 11 Dec 2024 06:31:55 GMT

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