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  4-year PhD Studentship: Antimicrobial resistance dynamics and antimicrobial use in wildlife rehabilitation facilities in the United Kingdom


   Bristol Veterinary School

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  Dr Fernando Sanchez-Vizcaino Buendia  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Antimicrobial resistance (AMR) is one of the greatest global public health threats of the 21st century (Prestinaci et al. 2015). To mitigate this urgent challenge, a One Health approach (i.e., with integrated actions across the human, animal and environmental interface) is needed. Of these dimensions, the role of the natural environment, and of wildlife species in particular in the emergence and dissemination of AMR, is still not well understood.

Injured and orphaned wildlife are often brought to wildlife rehabilitation facilities to be cared for with the ultimate goal of release back into the wild. This process can take days to months, and, during that time, these animals may receive antimicrobial therapy (Jorquera et al. 2021). One of the drivers of AMR emergence and dissemination is the use of antimicrobials in humans and animals, including wildlife in captive settings such as rehabilitation facilities (Holmes et al. 2016). There are current efforts to understand antimicrobial use in humans and domestic animals, but little information regarding captive wildlife.

Aims and objectives

The overarching goal of this project is to describe antimicrobial use practices and to characterize AMR in wildlife rehabilitation facilities in the UK. The specific aims for the PhD are:

Aim 1. Evaluate current antimicrobial use in wildlife rehabilitation facilities in the UK

Aim 2. Assess the emergence of AMR in wildlife species undergoing rehabilitation

Aim 3. Determine the genotypic profile of resistant Escherichia coli throughout the wildlife rehabilitation process

Methodology

Aim 1: We will survey a cross-section of UK wildlife rehabilitation facilities to understand antimicrobial prescription and AMR knowledge. Multivariable regression models will be used to determine the association between antimicrobial use and facility-related variables.

Aim 2: We will conduct a longitudinal study in wildlife rehabilitation facilities from South West England. Faecal samples will be collected upon admission, during rehabilitation, and before release, and examined for Escherichia coli. Antimicrobials tested will include those used at the rehabilitation facilities, as well as 3rd generation cephalosporins and fluoroquinolones, relevant for both human and veterinary medicine. Mixed effects models will assess differences in resistant E. coli levels over time.

Aim 3: Genomic DNA recovered from E. coli isolates will be subjected to whole genome sequencing (WGS). Analyses will include reference mapping to identify single nucleotide polymorphism (SNPs) for phylogenetic analysis and genomic assembly to identify the presence/absence of AMR genes. This will allow comparison with other E. coli WGS resistance patterns recovered from livestock, dogs, zoo animals, and humans in South West England leading to better understanding of AMR across One Health compartments.

The student will acquire skills in survey and study design, wildlife sample collection, microbiology, molecular epidemiology, and quantitative epidemiological methods.

Supervisors: Dr Fernando Sanchez-Vizcaino Buendia (primary supervisor), Dr Irene Bueno, Professor Kristen Reyher, Dr Nicola Rooney, Professor Matthew Avison, Dr Sion C Bayliss

Funding available

This project is open for Bristol PGR scholarship applications (closing date 1st December 2023)

The Bristol PGR scholarship funds tuition fees, the costs of carrying out your research and a maintenance stipend (at the minimum UKRI rate) for the duration of a PhD (four years).

How to apply for this project

This project will be based in Bristol Veterinary School in the Faculty of Health Sciences at the University of Bristol. Use this information to search for the relevant programme in our online application system.

Please visit the Faculty of Health Sciences website for details of how to apply, the information you must include in your application, and for information about our online Application Workshop to help you submit a competitive application.


Biological Sciences (4) Medicine (26) Veterinary Sciences (35)

References

Prestinaci, F., Pezzotti, P., & Pantosti, A. (2015). Antimicrobial resistance: a global multifaceted phenomenon. Pathogens and Global Health, 109(7), 309-318. https://doi.org/10.1179/2047773215Y.0000000030.
Jorquera, C. B., Moreno-Switt, A. I., Sallaberry-Pincheira, N., Munita, J. M., Navarro, C. F., Tardone, R., ... & Bueno, I. (2021). Antimicrobial resistance in wildlife and in the built environment in a wildlife rehabilitation center. One Health, 13, 100298. https://doi: 10.1016/j.onehlt.2021.100298.
Holmes, A. H., Moore, L. S., Sundsfjord, A., Steinbakk, M., Regmi, S., Karkey, A., ... & Piddock, L. J. (2016). Understanding the mechanisms and drivers of antimicrobial resistance. The Lancet, 387(10014), 176-187. https://doi.org/10.1016/S0140-6736(15)00473-0.

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 About the Project