RodentGate
Post-Doc·2022–2024
Molecular investigation of rodent-borne pathogens and their transmission risks to pig and poultry production systems.
Dr Hayley Thompson
BSc (Hons), PhD
Lecturer in Food Science
Food and Markets Department
Dr Hayley Thompson joined the Natural Resources Institute in 2022 and is currently a Lecturer in Food Science within the Food and Market Department. Her work sits at the interface of food microbiology, microbial ecology and One Health, with a particular focus on antimicrobial resistance and pathogen transmission across food and environmental systems.
Hayley trained as a molecular microbiologist at King’s College London, where she completed her PhD investigating virulence determinants in the periodontal pathogen Tannerella forsythia. She subsequently held postdoctoral roles at King’s College London and Queen Mary University of London, contributing to internationally funded research on the human oral microbiome, microbial cultivation of previously uncultured bacteria and in vitro biofilm modelling, in collaboration with academic and industrial partners.
At NRI, Hayley initially worked as a molecular microbiologist on the RodentGate project, leading molecular and sequencing‑based investigations of rodent‑borne pathogens and their relevance to livestock and food systems. In November 2024, she transitioned into a lectureship, where she now integrates research leadership, postgraduate supervision and teaching across food microbiology, food safety and One Health. Hayley’s current work contributes to interdisciplinary collaborations across the UK, Europe and South Africa, advancing molecular surveillance, AMR mitigation and One Health approaches to food system resilience.
Hayley’s research focuses on foodborne, environmental and zoonotic pathogens, with particular emphasis on One Health approaches to antimicrobial resistance and pathogen transmission across food, agricultural and environmental systems. Her work integrates molecular microbiology with microbial ecology to address challenges at the wildlife–livestock–plant–food interface, including the surveillance and control of emerging and neglected pathogens relevant to food safety and public health.
Hayley applies sequencing‑based and computational approaches to investigate microbial communities, antimicrobial resistance and pathogen transmission across food and environmental systems. Her expertise includes the analysis and interpretation of 16S rRNA gene amplicon sequencing, shotgun metagenomics and whole‑genome sequencing (WGS) data to characterise microbial diversity, functional potential and pathogen population structure. These approaches support molecular surveillance, resistome analysis and comparative genomics and are integrated with ecological and epidemiological data within applied One Health research and food safety contexts.
Hayley’s research aims to generate actionable evidence for food system stakeholders, informing biosecurity practices, AMR monitoring frameworks and sustainable pathogen management strategies across agricultural and community settings Hayley is a member of the Behavioural Ecology Research Group and the Food Safety Research Group.
OHRatSA
Co-I · SAMRC · 2025–2028
A One Health approach to managing rodent pests impacting human health and wellbeing in South African townships.
IOSAR
Co-PI · SAMRC · 2025–2028
Integrated One Health Surveillance for Antimicrobial Resistance, addressing AMR across agricultural, environmental and community settings.
Antimicrobial resistance in the livestock–wildlife–plant–food nexus
PI · REF & Food Safety and Quality Research Group funding · University of Greenwich · 2023
Exploration of integrated multi-omics approaches in microbiome science in the food system
Co-PI · REF & Food Safety and Quality Research funding · University of Greenwich · 2024
Development of an NRI-led HPC and bioinformatics training programme
PI · HEIF · University of Greenwich · 2025
Investigating Aliarcobacter spp. from a mixed pig-arable farm
Co-PI · REF funding · University of Greenwich · 2025
- Hope Okon, PhD (Co‑Supervisor): Community ecology of bacteria and the role of rodent reservoirs | University of Greenwich | 2022 - present
- Ainhoa Rodriguez Pereira, PhD (Co‑Supervisor): Unravelling the host–vector–pathogen interplay of Plasmodium and Anopheles | LIDo DTP PhD student, University of Greenwich | 2023 - present
- Sheldon Viviers, PhD (Co‑Supervisor): Affiliated with the IOSAR project | University of Pretoria | 2025 - present
- Ghayyoor Sultan, PhD (Co‑Supervisor): Affiliated with the IOSAR project | University of Greenwich | 2026 – present
- Supervisor of multiple MSc independent research projects aligned with food microbiology, antimicrobial resistance (AMR), molecular detection methods and microbiome analysis.
Hayley integrates research-led teaching and practical laboratory training into her modules on the MSc Applied Food Safety and Quality Management programme:
- Food Microbiology (MICR1005) - Module Leader
- MSc Independent Research project (FOOD 1005) - Deputy Module Leader & Project Supervisor
- Research Methods (ENVI1096) - Lecturer
- Food Safety (FOOD 1025) - Lecturer
And the BSc Biology programme:
- Microbiology and the Environment (MICR 1009) - Lecturer
Member of the Microbiology Society
Dr Hayley Thompson joined the Natural Resources Institute in 2022 and is currently a Lecturer in Food Science within the Food and Market Department. Her work sits at the interface of food microbiology, microbial ecology and One Health, with a particular focus on antimicrobial resistance and pathogen transmission across food and environmental systems.
Hayley trained as a molecular microbiologist at King’s College London, where she completed her PhD investigating virulence determinants in the periodontal pathogen Tannerella forsythia. She subsequently held postdoctoral roles at King’s College London and Queen Mary University of London, contributing to internationally funded research on the human oral microbiome, microbial cultivation of previously uncultured bacteria and in vitro biofilm modelling, in collaboration with academic and industrial partners.
At NRI, Hayley initially worked as a molecular microbiologist on the RodentGate project, leading molecular and sequencing‑based investigations of rodent‑borne pathogens and their relevance to livestock and food systems. In November 2024, she transitioned into a lectureship, where she now integrates research leadership, postgraduate supervision and teaching across food microbiology, food safety and One Health. Hayley’s current work contributes to interdisciplinary collaborations across the UK, Europe and South Africa, advancing molecular surveillance, AMR mitigation and One Health approaches to food system resilience.
Hayley’s research focuses on foodborne, environmental and zoonotic pathogens, with particular emphasis on One Health approaches to antimicrobial resistance and pathogen transmission across food, agricultural and environmental systems. Her work integrates molecular microbiology with microbial ecology to address challenges at the wildlife–livestock–plant–food interface, including the surveillance and control of emerging and neglected pathogens relevant to food safety and public health.
Hayley applies sequencing‑based and computational approaches to investigate microbial communities, antimicrobial resistance and pathogen transmission across food and environmental systems. Her expertise includes the analysis and interpretation of 16S rRNA gene amplicon sequencing, shotgun metagenomics and whole‑genome sequencing (WGS) data to characterise microbial diversity, functional potential and pathogen population structure. These approaches support molecular surveillance, resistome analysis and comparative genomics and are integrated with ecological and epidemiological data within applied One Health research and food safety contexts.
Hayley’s research aims to generate actionable evidence for food system stakeholders, informing biosecurity practices, AMR monitoring frameworks and sustainable pathogen management strategies across agricultural and community settings Hayley is a member of the Behavioural Ecology Research Group and the Food Safety Research Group.
RodentGate
Post-Doc·2022–2024
Molecular investigation of rodent-borne pathogens and their transmission risks to pig and poultry production systems.
OHRatSA
Co-I · SAMRC · 2025–2028
A One Health approach to managing rodent pests impacting human health and wellbeing in South African townships.
IOSAR
Co-PI · SAMRC · 2025–2028
Integrated One Health Surveillance for Antimicrobial Resistance, addressing AMR across agricultural, environmental and community settings.
Antimicrobial resistance in the livestock–wildlife–plant–food nexus
PI · REF & Food Safety and Quality Research Group funding · University of Greenwich · 2023
Exploration of integrated multi-omics approaches in microbiome science in the food system
Co-PI · REF & Food Safety and Quality Research funding · University of Greenwich · 2024
Development of an NRI-led HPC and bioinformatics training programme
PI · HEIF · University of Greenwich · 2025
Investigating Aliarcobacter spp. from a mixed pig-arable farm
Co-PI · REF funding · University of Greenwich · 2025
- Hope Okon, PhD (Co‑Supervisor): Community ecology of bacteria and the role of rodent reservoirs | University of Greenwich | 2022 - present
- Ainhoa Rodriguez Pereira, PhD (Co‑Supervisor): Unravelling the host–vector–pathogen interplay of Plasmodium and Anopheles | LIDo DTP PhD student, University of Greenwich | 2023 - present
- Sheldon Viviers, PhD (Co‑Supervisor): Affiliated with the IOSAR project | University of Pretoria | 2025 - present
- Ghayyoor Sultan, PhD (Co‑Supervisor): Affiliated with the IOSAR project | University of Greenwich | 2026 – present
- Supervisor of multiple MSc independent research projects aligned with food microbiology, antimicrobial resistance (AMR), molecular detection methods and microbiome analysis.
Hayley integrates research-led teaching and practical laboratory training into her modules on the MSc Applied Food Safety and Quality Management programme:
- Food Microbiology (MICR1005) - Module Leader
- MSc Independent Research project (FOOD 1005) - Deputy Module Leader & Project Supervisor
- Research Methods (ENVI1096) - Lecturer
- Food Safety (FOOD 1025) - Lecturer
And the BSc Biology programme:
- Microbiology and the Environment (MICR 1009) - Lecturer
Member of the Microbiology Society