This project contributes towards two important societal needs, (1) maintaining clean water, and (2) limiting the further evolution and spread of AMR in freshwater ecosystems. Antibiotic-resistant bacteria are projected to become one of the greatest emerging challenges to healthcare and agriculture settings worldwide. Prevalence of AMR in freshwater environments is a growing threat for human wellbeing (maintaining access to clean water for direct or indirect consumption) and healthcare (limiting the evolution and spread of AMR). Freshwater AMR is also impacting agriculture and veterinary settings, plus could have large impacts on recreation (fisheries, bathing). Despite this large societal importance, relatively little is known about the distribution and prevalence of AMR in UK freshwaters. The key challenge from our stakeholders is to provide research-based evidence on the prevalence and drivers of environmental AMR, to aid them in developing evidence-based policy and environmental management strategies.
Project Aims and Methods
Monitoring AMR in freshwater habitats is complicated by water flow and sediment transport, since both factors continuously lead to a redistribution of water and dissolved substances and particles, along with any AMR microbes found at a given site. This can lead to AMR tests of the water body or local sediment to produce patchy and hard to interpret results, with high spatial and temporal variability that may in fact be due to sampling artefacts. A biomonitoring approach, where freshwater taxa are screened for presence of AMR in their guts, may produce a more consistent signal, since this would integrate across larger spatial and temporal scales. However, there is little known about the efficacy of this approach for AMR monitoring. To this end, this proposal will investigate the possibility of using various animal taxa to detect AMR, in order to capture different trophic levels and scales of animal mobility. The student will develop their own research ideas, based upon this goal. Resources and methods available include field sampling across catchments (e.g. sediment, biota), metagenomic analysis, as well as culture and PCR-based assays of various environmental samples. This might be supplemented with qPCR and/or whole-genome sequencing of strains of interest. We aim to collect and screen sediment samples and spatially matched fresh biological samples from benthic invertebrates, non-migratory fish, and faecal (spraint) samples from otters, along river catchments – allowing us to test AMR detectability on three trophic levels and in animals with different movement radii. We will explore the efficacy of assays for archived otter faecal samples (Cardiff University Otter Project), which would allow retroactive screening of freshwater habitats across the UK based on >3000 samples collected since 1992. Results will be analysed in a spatially explicit context, making use of catchment and river bed data on sediments, flow and surrounding habitats, using GIS. We hypothesise that the effect on microbial communities of runoff from animal husbandry will be detectable in adjacent freshwater habitats and their inhabitants, and perhaps especially so at higher tropic levels.
Candidate requirements
Skills in microbiology, bioinformatic analysis and or statistical modelling would be advantageous. The PhD will provide training where relevant.
Candidates must meet the Cardiff University PhD entry requirements - click on 'Institution Website' for details.
Project partners
Drs F Hailer and E Chadwick (Cardiff University) provide access to otter samples and data (1992-present) and expertise in genomics, genetic assay development, and digital mapping/statistical modelling. Dr A Singer, GW4 co-supervisor based at CEH specialises in drivers of environmental AMR using genomic approaches. Prof Feil’s research focuses on areas including antibiotic resistance, wastewater microbiology, and metagenomics. Together, the supervisory team provide highly complementary skills which will provide methodological, practical, and intellectual support appropriate to the aims of the project. The wider collaborative network of the team members brings further links to ensure policy relevance (links to DEFRA) and the One-Health approach to integrative human, wildlife, and veterinary health.
Training
The PhD student will be trained in sample collection in the field, incl. sediment, benthic invertebrates, fish, and fresh otter spraint samples; microbiology laboratory skills for culturing and isolating AMR bacteria, phenotypic classification, next-generation sequencing; phylogenetics and sequence annotation; PCR-based screening of environmental samples for strains detected in the previous steps; analysis of landscape / river catchment data using GIS, statistical analysis/modelling in ‘R’.
How to Apply
The start date of this studentship is October 2022. To submit a formal application via Cardiff University’s online application service, click the 'Institution Website' button on this advert; in the ‘Apply’ box at the top-right of the page, select Qualification (Doctor of Philosophy), Mode of Study (Full Time) and Start Date (October 2022). This will take you to the application portal.
Candidates must submit the following:
• Supporting statement
• CV
• Qualification certificates
• Proof of English language (if applicable)
In the research proposal section of the application, specify the project title and supervisors of the project. In the funding section, select “I will be applying for a scholarship/grant” and specify advertised funding from NERC GW4. If you are applying for more than one Cardiff University project, please note this in the research proposal section as the form only allows you to enter one title.
The application deadline is Monday 10 January 2022 at 2359 GMT. Interviews will take place from 23rd February to 9 March 2022. For more information about the NERC GW4+ Doctoral Training Partnership please visit https://www.nercgw4plus.ac.uk.
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