Dr Fernando Sanchez-Vizcaino Buendia (primary supervisor), Dr Irene Bueno
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
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.
Apply for this project
This project will be based in Bristol Veterinary School.
Please contact firstname.lastname@example.org for further details on how to apply.