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Biomonitoring of Antimicrobial Resistance in UK Freshwater Ecosystems: An Integrated Microbiological and Genomic Approach

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  • Full or part time
    Dr Frank Hailer
    Dr E Chadwick
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description


Successful treatment of bacterial infections is paramount in healthcare, veterinary medicine, animal husbandry and agriculture, yet extensive use of antibiotics is driving selection for antimicrobial resistance (AMR).

While the AMR mechanisms are a natural phenomenon, spill-over from anthropogenic settings is believed to be leading to the accumulation and global spread of AMR. This can lead to further evolution of AMR strains through vertical transmission or horizontal gene transfer to previous non-AMR strains. This poses a severe threat when strains are mobilised back into healthcare, veterinary or agricultural settings.

Project aims and methods

This project will pursue an integrated microbiological and genomic biomonitoring approach, surveying UK freshwater environments for anti-microbial resistance (AMR).

First, we will conduct broad-target screening to compare the prevalence of live AMR cultures in freshly collected animal guts with that in sediments at the same location. Biomonitoring will be done at three trophic levels: benthic invertebrates, non-migratory fish, otters.

Second, obtained live AMR strains will be tested phenotypically and undergo whole-genome sequencing for phylogenetic and functional analysis. Thirdly, we will develop and apply high-throughput environmental screening approaches (based on the obtained knowledge of UK freshwater AMR strains), testing a larger sample of fresh environmental samples across the UK.

Finally, we will apply these screening methods to archived animal gut samples, exploring trends in freshwater AMR across time and space.

Sampling will focus on being able to determine the impact of AMR deriving from agriculture and animal husbandry, since the other main source for freshwater AMR, human wastewater, has already been studied previously at much greater detail. Specifically, we will investigate areas with runoff from high- and low-intensity livestock farming.


You will spend around one month per year with partner organisations (Centre for Ecology and Hydrology, Uppsala University), undertaking all research steps from field collection of abiotic and biological samples (Cardiff University, Centre for Ecology and Hydrology) to analytical microbiology (Cardiff, Centre for Ecology and Hydrology), genomics and development of genetic screening methods (Cardiff, Centre for Environment, Fisheries and Aquaculture Science, Uppsala University), spatial analysis and statistical modelling (Cardiff, Centre for Ecology and Hydrology).


You will be trained in sample collection in the field, including sediment, benthic invertebrates, fish, and fresh otter spraint samples. You will gain experience with microbiology laboratory skills for culturing and isolating AMR bacteria, phenotypic classification, next-generation whole-genome sequencing of resistant isolates to conduct phylogenetics and sequence annotation.

Funding Notes

A studentship will provide UK/EU tuition fees, a stipend in line with the RCUK rate (£14,553 per annum for 2017/18) and a generous budget for research expenses and training.

UK Research Council eligibility conditions apply, please get in contact for more details.

How good is research at Cardiff University in Biological Sciences?

FTE Category A staff submitted: 54.70

Research output data provided by the Research Excellence Framework (REF)

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