Nanopore sequencing to investigate zoonosis and antibiotic resistance at the wildlife - livestock interface

Project summary
We are becoming increasingly aware that human, veterinary and environmental health are intrinsically linked. Both farming and food production systems must not only be resilient to environmental changes and threats but the systems themselves must also perform with minimal environmental impact. Climate change events such as flooding and increased temperatures are predicted to bring additional unknown challenges and therefore methods to rapidly and comprehensively characterise microbial risks are vital. Furthermore, farmers are striving to develop sustainable practices that reduce GHS emissions and it is important that these new approaches also limit microbial transmission.
This project takes a "One Health" approach by focussing on the interface between wildlife and livestock with a major emphasis on the transmission of zoonotic disease and antimicrobial resistance (AMR) genes. Foodborne pathogens do not often cause overt disease in animals but can be transmitted through the food supply chain and cause human disease. In the same way, AMR genes can potentially be transmitted between wildlife and livestock species and spread to humans. Additionally, some wildlife species act as indicators of environmental health and resilience. By understanding and monitoring contamination of these sentinel species we can more fully understand the impact of pressures such as microbial contaminants arising from farming.
Previously, conventional, targeted methods such as laboratory culture and PCR have been used to monitor carriage of bacteria and viruses by animal species. In recent years, development of 3rd generation sequencing technologies has enabled enhanced microbe detection due to the ability to sequence long reads. The key aim of this project is to apply and assess this novel technology to investigate the presence of microbial species and AMR genes within two wildlife populations which represent different dynamics between wildlife and livestock.
Firstly, wild bird populations in close proximity to farms1 will be investigated to assess transmission of zoonotic pathogens and AMR genes to livestock. Secondly, grey seals, which are an important sentinel species for coastal marine health, will be investigated to assess environmental microbial contamination. We have previously detected microbial pathogens within grey seal populations as a result of anthropogenic activity2,3, as well as AMR genes in seals and bird populations.
The student will optimise and develop laboratory and bioinformatics methods in Nanopore sequencing and evaluate the presence of zoonotic pathogens and AMR genes within wildlife populations. Results will be compared with data from livestock and relevant environmental samples to identify potential transmission routes. Nanopore sequencing outputs will also be compared with gold-standard laboratory methods for pathogen and AMR detection to assess application of Nanopore technology as a surveillance tool.
The student will be based at Moredun Research Institute, which is situated just outside Edinburgh. The supervisory team will provide training and expertise in zoonotic pathogens, AMR and Oxford Nanopore Technologies, (Moredun and University of Aberdeen), sequence analysis and bioinformatic pipelines (Biomathematics and Statistics Scotland (BioSS)).