Fellowships

This fellowship focuses on creating a public-facing dashboard to visualise AMR in aquaculture. The project will use existing data to develop a proof-of-concept platform. This tool is intended to help policymakers, researchers, and the public to better understand the dynamics of AMR in aquatic systems.

Objectives: The primary objective of this fellowship is to develop a data visualisation platform for AMR in aquatic environments. The platform will integrate metagenomic sequencing data with hydrological and chemical data from various locations in Southeast China. To ensure the dashboard is effective, we will conduct surveys with potential users to identify their specific needs. We will also collaborate with epidemiologists and other experts to ensure the data is interpreted and presented in a clear and meaningful way.

Progress: The project successfully coordinated the collection of data, including sequencing information, from two distinct seasons. Initial meetings have been held with our collaborators to discuss the data we have gathered and to begin shaping the preliminary design of the dashboard. A comprehensive questionnaire has been prepared and is ready to be distributed to various stakeholders. The feedback from this survey will be crucial in refining the dashboard's features and content. Furthermore, we have started to build our technical capabilities by undertaking training in data dashboarding techniques, with valuable support from our industry partner, Arup.

Impact: This project is expected to have a significant impact by enhancing the understanding of AMR in aquatic environments among policymakers, industry professionals, and the general public. The main outcome of the fellowship will be a functional prototype of an online AMR dashboard. This prototype will serve as a blueprint for the future development of a more comprehensive and scalable visualisation tool. The project should also foster stronger collaborations between academic researchers and industry experts, creating a foundation for future joint initiatives.

With the help of this Fellowship, Ioannis was able to visit two research laboratories in January 2025, Professor’s Monica J. Pajuelo’s in Lima Peru (20/1/2025 – 31/1/2025) and Professor Davey Jones’s in Bangor (13/1/2025 – 18/1/2025). During these visits, he was able to get hands on experience in wastewater collection, DNA extraction from wastewater and clinicalisolates, whole genome sequencing and metagenomic sequencing, as well as bioinformatic analysis. With this work, he was able to generate preliminary data on how to optimize DNA extraction from wastewater.

Objectives: Perform two research visits in collaborating laboratories in order to improve research skills in areas relevant to wastewater surveillance of AMR.

Progress: Both visits were performed in January 2025. Professor’s Monica J. Pajuelo’s in Lima Peru (20/1/2025 – 31/1/2025) and Professor Davey Jones’s in Bangor (13/1/2025 –18/1/2025).

Impact: During the visits Ioannis was able to gain hands on experience in the following areas: wastewater collection using grab samples, wastewater collection using automated pumps, wastewater processing using centrifugation, wastewater processing using membrane filtration, DNA extraction from wastewater using the QIAGEN DNA Soil Kit , DNA extraction from clinical isolates using the Oxford Nanopore Rapid Barcoding Kit V14, Metagenomic Library preparation using the Oxford Nanopore Ligation Kit, Metagenomic sequencing using Oxford Nanopore PromethION, culture of bacteria from wastewater on selection media.

During the visits, Ioannis was able to network with Dr Reshma Silvester, Professor Davey Jones, Professor Monica Pajuelo and Omar Alonso Romero Rodriguez and establish an ongoing collaboration in AMR-related research.

Impact: Preliminary data for Ioannis’s Fellowship application was created. Two scientific publications are currently being written up using the data.

Wastewater-based epidemiology (WBE) has emerged as a valuable public health tool, offering a non-invasive approach to monitor population-level health indicators. This 6-month fellowship aimed to leverage WBE to address a critical knowledge gap in AMR surveillance within hospitals in Wales, focusing on carriers of clinically relevant AMR genes, within the ESKAPEE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli.

Objectives: Construct metagenome-assembled genomes (MAGs) of ESKAPEE pathogens from hospital wastewater. Identify and characterise AMR genes within these pathogens, broadening the understanding of the resistome carriers in healthcare settings. Directly compare wastewater resistomes with genomic data from clinical isolates, where available, and with publicly available data on phenotypic markers of AMR in clinical samples.

Progress: The pipeline has been set up on the Supercomputing Wales platform and is currently processing archived hospital wastewater metagenomic datasets from three major hospitals in North Wales. Downstream analysis of the MAG bins has begun, focusing on identifying AMR genes within recovered MAGs.

Impact: This fellowship has provided a valuable platform to expand professional network and initiate cross-sectoral collaborations. Engaging with healthcare professionals and public health authorities has been particularly impactful. Reshma already had some productive discussions with healthcare professionals from Public Health Wales, including Dr Noel Craine, Public Health Wales, Bangor Hospital, which are helping to align the research with ongoing clinical and surveillance efforts. These interactions have laid the groundwork forfuture collaborative research and integration of wastewater AMR surveillance into broader public health strategies.

This fellowship/internship aims to identify the factors influencing the effectiveness of AMR dashboards, with data validity and usability as the main evaluation criteria. This will be done through content analysis of existing literature. Identifying these factors will facilitate the exchange of the complex data comprising AMR research and applications.

Objectives: Analyse existing AMR dashboards, covering environmental health, animal health and human health, using theories from usability, accessibility and user engagement. Compare the differences between AMR dashboards focusing on environmental health, animal health and human health. Work with clinical infection and public health teams to identify design considerations for their use cases.

Impact: A catalogue of current publicly available AMR dashboards. Enhanced understanding of AMR and the need for data dashboards for understanding AMR in environmental health, animal health and human health. A framework that outlines the design considerations that make a dashboard effective for various user groups. This project will also advance AMR surveillance in one health and provide evidence on effective actionable data dashboards for antimicrobial stewardship.

Data-based technologies have the potential to inform antimicrobial stewardship and infection prevention control across clinical settings. However, this potential can only be realised if people adopt and use these technologies, leading to changes in behaviour and practice. This 6-month fellowship aims to bridge this gap by exploring the factors influencing the use of digital, data-driven innovations for antimicrobial stewardship (AMS) and infection prevention and control (IPC) and identifying strategies to enable their uptake, contributing to GC 2.1 and 2.2.

Objectives: Through qualitative interviews with healthcare workers across selected wards within UCLH NHS Foundation Trust the planned fellowship will aim to: (1) Investigate healthcare worker attitudes towards, and perceived acceptability of, the use of routine healthcare data and a wearable device for collecting movement data to inform infection prevention control and antimicrobial stewardship. (2) Explore antimicrobial prescribing feedback might best support clinical teams through understanding healthcare workers’ perspectives on how, when and in what format feedback on antimicrobial prescribing practice could be most useful. (3) Investigate how data could be used to inform practice and decision making to inform overall infection prevention control and antimicrobial stewardship.

Progress: Inter-disciplinary collaborations have been set up and NHS ethics protocol developed and recently approved. Through team discussions and informed by behavioural science frameworks, potential interview questions have been developed.

Impact: This fellowship will provide evidence on how best to optimise the use of digital health technologies and interventions which tackle AMR, and identify sustainable strategies for their successful implementation, ensuring they are adopted, trusted, and used effectively across different healthcare settings, enabling the design and optimisation of their use in real-worldsettings. Research outputs will be developed and disseminated based on the findings for the project such as peer-reviewed journal article(s) for publication, internal and/or external summaries and presentations of the information to inform practices, knowledge sharing and future research informing digital health solutions for AMR.

This Fellowship explores the integration of pathogen whole genome sequencing (WGS) into the Northen Ireland Public Health Agency’s (NIPHA) AMR surveillance system. Through stakeholder engagement and system mapping, the project will recommend scalable data management solutions, define workflows for genomic processing and AMR gene detection, and propose interface and visualisation designs that align with public health needs. The outcomes will support evidence-based planning for future genomics integration, ensuring that NIPHA’s AMR surveillance is equipped to harness emerging technologies for improved public health decision-making.

Objectives: This project aims to explore the integration of pathogen genome sequencing into PHA’s AMR surveillance framework. The focus is on defining the technical and functional requirements for a surveillance system that can incorporate genomic data from diverse bacterial species, from raw sequence generation to bioinformatics analysis, storage, and reporting.

Impact: A clear mapping of the bioinformatics and surveillance process, from raw data collection to actionable public health insights. A set of functional and technical specifications, including design concepts for system interfaces, visualisations, and integration. Guidance on bioinformatics tools, data storage solutions, and integration strategies that align with PHA’s capacity and needs. A presentation that communicates key findings, user requirements, and design recommendations to support future planning and decision-making.

This fellowship investigates the diversity and prevalence of human pathogenic fungi (predominantly belonging to Candida spp.) and antifungal-resistant (AFR) genes in wastewater networks, with a focus on the environmental factors that influence their distribution and persistence. Using metagenomic datasets, it explores the emergence, prevalence and spread of antifungal resistance in these systems, aiming to address a significant gap in current research, which has predominantly focused on clinical environments.

Objectives: This project aims to bridge this gap by exploring wastewater as both a reservoir and a conduit for the spread of antifungal-resistant fungi. It also aim to develop standardised methods for monitoring fungal pathogens, such as C. auris, C. krusei, C.albicans, C. parapsillosis and AFR genes in environmental settings, using wastewater-based epidemiology (WBE), a tool that could potentially be adapted for tracking fungal outbreaks in the environment.

Impact: Standardised methods for monitoring fungal pathogens using WBE. Insights into the role of wastewater and environmental waters in the global antifungal resistance crisis, focusing on the environmental factors that drive resistance dynamics and their implications for public health.