IAP-24-048

Reservoirs of Bacterial Pathogens in Captive Animal Enclosures: Evolutionary Drivers in a Changing Climate

Background:
Bacterial pathogens, including those with multidrug resistance (MDR), form biofilms on a range of materials in the environment, such as soil, and organic wastes. Such biofilms enhance the environmental persistence of pathogens and their ability to tolerate environmental stresses, e.g., UV irradiance and extremes of temperature. Climate change is exacerbating these dynamics by altering temperature, humidity, and other environmental factors, which can influence pathogen persistence, virulence, and antimicrobial resistance (AMR) patterns (Fig. 1). In captive animal enclosures (e.g., zoos and wildlife parks), this dynamic can be amplified, as pathogens in bedding, and water sources may cycle between the captive animals and the environment (e.g., in faeces and wastes removed from the enclosure). Importantly, wild birds, rodents, and other wildlife can also transfer pathogens between the enclosure and the environment compounding the complexity of disease transmission. Furthermore, symptomatic animals can also shed pathogens (with or without drug resistance), creating a heightened risk of infection or secondary infections to other animals, particularly those that are immunocompromised or under stress from breeding or moulting (Fig. 2).

Aims:
By understanding pathogen reservoirs, AMR dynamics, and transmission routes, the overarching aim of this project is to identify critical surfaces and conditions that promote pathogen survival to pinpoint essential control points where targeted interventions can mitigate the risk of pathogen transmission. This research will ultimately inform the development of biosecurity protocols that are resilient to the impacts of climate change, contributing to improved animal welfare and optimised husbandry practices within controlled environments.

Research objectives:
1. Through comprehensive temporal surveying, identify anthropogenic and natural materials that are reservoirs of bacterial pathogens in captive animal enclosures.
2. Quantify the levels of AMR in the captive animal environment, and correlate with antimicrobial use.
3. Using molecular methods, compare isolates recovered from each material and animal throughout the sampling period to determine potential routes of transmission.
4. Quantify the impact of climate change projections on pathogen persistence, virulence and AMR dynamics.

This work will take place both in controlled laboratory settings at the University of Glasgow and on-site at selected Royal Zoological Society of Scotland (RZSS) locations, including Edinburgh Zoo and the Highland Wildlife Park.
The student will conduct monthly sampling over the course of a year at fixed high-contact areas within enclosures (e.g., feeding stations, substrates where animals rest) and across a range of environmental materials (e.g., wood, vegetation, water, and soil) to quantify pathogen presence, load, and distribution. In parallel, environmental samples from outside the enclosures, collected from similar materials, will help the student understand potential external contamination sources. At each monthly sampling timepoint, faecal samples from animals housed in each examined enclosure will be collected and analysed to determine their role as symptomatic or asymptomatic carriers of a range of target pathogens. Any animal displaying signs of infection (e.g., gastrointestinal, skin, or wound infections) will be dynamically sampled. Environmental variables such as temperature and rainfall will be monitored throughout the study to correlate these factors with pathogen persistence on different surfaces across seasons.
In addition to identifying the presence and persistence of pathogens, we will examine the presence of AMR and MDR among the bacterial isolates. This will provide critical insights into how resistant pathogens may survive and spread in captive environments, informing zoo practices and decisions around animal treatment and antibiotic use. To complement fieldwork, the student will replicate environmental conditions in the laboratory, including extreme climate scenarios, to assess how pathogens persist and maintain virulence across various materials under different conditions.
This research will culminate in a comprehensive risk assessment, offering critical insights into pathogen survival, AMR, and MDR in relation to material type and environmental conditions. By integrating field and laboratory data, the student will draw conclusions about the role of different surfaces as reservoirs for bacterial pathogens and antibiotic-resistant strains, generating evidence-based recommendations for biosecurity and enclosure management practices. The findings will be disseminated through peer-reviewed publications and shared with veterinarians, wildlife managers, and other stakeholders. Based on the results, the student will develop guidelines to manage environmental reservoirs of bacterial pathogens in captivity, addressing key areas such as enclosure material selection, cleaning protocols, and overall environmental management to enhance animal welfare, mitigate infection risks, and guide effective antibiotic use. Training sessions will be developed for zookeepers and wildlife managers, equipping them with the knowledge and tools to implement the recommended biosecurity measures effectively. All aspects of the research will adhere to stringent ethical guidelines, ensuring minimal disruption to the animals and their habitats while prioritising animal welfare throughout the study.

Year 1

In the first few months (Months 1-6), the focus will be on building foundational knowledge and setting the groundwork for the project. A comprehensive literature review will be conducted on pathogen persistence, AMR, and environmental reservoirs in captive settings. During this time, the student will also familiarise themselves with the research environment and protocols, collaborating with CASE partners at RZSS to design project methodologies. Field visits to RZSS sites will take place to establish sampling schedules and finalise sampling locations, allowing for engagement with zookeepers and veterinary teams to refine pathogen monitoring techniques. Some pilot testing of sampling techniques and environmental monitoring tools may be conducted to refine protocols. From Month 7 onward, the student will begin collecting initial samples and conducting preliminary laboratory simulations to examine how environmental conditions, including enhanced scenarios, influence pathogen persistence and virulence. The focus will remain on gradually familiarising the student with these processes and adjusting the approach as needed.

Year 2

In Year 2 (Months 13-18), the project will enter a more structured phase, with ongoing monthly sampling now being implemented consistently to capture seasonal variations. During this period, smaller-scale data analysis will begin, focusing on early findings on pathogen presence and environmental factors as well as characterising bacterial pathogens, with an emphasis on virulence genes, AMR, and MDR profiling. Rather than a singular block of analysis, this stage will emphasise building on initial findings to inform the ongoing data collection process.
From Months 19-24, more in-depth analysis will begin, alongside the finalisation of sampling. Early manuscript writing or chapter drafting should be encouraged as results become clearer, allowing the student to engage with data at a manageable pace while building towards publications.

Year 3

In Year 3, data analysis will continue as the student integrates their findings. This approach will offer a more comprehensive understanding of how environmental factors impact pathogen persistence and resistance. From Months 25-30, focused analysis will continue, particularly evaluating environmental factors like temperature and humidity in relation to pathogen survival and AMR profiles. The three-month placement with RZSS, now scheduled for Months 31-33, will provide an opportunity to conduct an additional in situ environmental project, focusing on environmental sampling and monitoring in zoo settings. The placement will also serve as a time to refine biosecurity recommendations, using real-world insights on environmental factors that influence pathogen persistence and transmission in captive environments. After the placement, the student will begin drafting guidelines and conducting risk assessments based on the cumulative analysis of data from different environments, building toward manuscripts. By staggering manuscript preparation throughout the project, the student can be encouraged to work on drafts as they go, reducing the burden in the final months.

Year 3.5

In the final months (Months 37-42), the focus will be on completing publications, engaging with stakeholders, and preparing the student-led workshop. The student will finalise their research findings and submit manuscripts to peer-reviewed journals, leveraging the drafts prepared throughout the project. Stakeholder engagement and training sessions for zookeepers and wildlife managers will also be a priority, ensuring the project’s findings are translated into practical applications for zoo management and animal welfare. The final workshop will serve as a platform to present findings and encourage dialogue on the implications for biosecurity in captive environments.

This studentship will provide a platform to build an interdisciplinary research career in One Health sciences. Extensive skill development in field and lab work will include comprehensive training in sampling and monitoring techniques, while the student will also benefit from working closely with members of One Health Research into Bacterial Infectious Diseases (OHRBID) team at the University of Glasgow where they will gain skills in general and molecular microbiology. Specialist training in the safe handling of Hazard Group 2 microorganisms will be provided by the supervisory teams at both Glasgow and Stirling. During the first year, the student will learn key laboratory analytical skills for quantifying pathogenic bacteria and determining AMR and MDR profiles; before continuing with more advanced molecular and sequence-based skills in years 2 and 3. The student will also become proficient in the collection and handling of both environmental and veterinary samples.
A key aspect of the project will be a three-month placement with the RZSS, where the student will focus on environmental sampling, pathogen monitoring, and biosecurity measures within zoo and wildlife park settings. This placement will provide hands-on experience in field data collection and offer practical insights into managing environmental factors that influence pathogen persistence and transmission, aligning with the project’s focus on environmental reservoirs and AMR in captive environments. This placement will provide the student with valuable skills in data collection, pathogen monitoring, and biosecurity measures, while fostering the development of transferable skills such as teamwork, project management, and effective communication. These experiences will be critical in building the student’s professional competencies, with direct applications to both the academic and practical aspects of One Health research.