A Data-driven approach for prioritising and assessing risks of microbial and chemical contaminants in dairy products across Europe

Abstract

Dairy products play a significant role in global diets, supplying key nutrients like proteins, calcium, and vitamins for people worldwide, with more than six billion individuals relying on dairy products as part of their daily diet. The European Union contributes approximately 160 million tonnes to global milk production annually, highlighting the dairy sector’s broader role beyond nutrition, including its role in livelihoods and the wider economy across the agri-food supply chain. However, the dairy industry faces persistent food safety challenges linked to microbial and chemical contamination, particularly from pathogens like Listeria monocytogenes, Escherichia coli, and Salmonella spp., and chemical hazards such as aflatoxins, lead, and cadmium. These risks are exacerbated by climate change, which influences storage temperatures, microbial behaviour, and the conditions under which contamination may flourish or be mitigated. In this thesis, a data-informed approach is developed to assess and prioritise microbial and chemical risks in dairy products across Europe, focusing on environmental and demographic variability. It begins with a detailed review of current food safety risk assessment frameworks, identifying limitations in how climate change is incorporated and examining the utility of open-source databases such as WHO GEMS/Food and RASFF. A prioritisation model was developed using machine learning algorithms, including decision trees and support vector machines, to rank microbial and chemical hazards based on toxicity, prevalence, and exposure. The results identified Listeria monocytogenes, E. coli, and Salmonella spp. as key microbial risks. At the same time, aflatoxin B1, lead, and cadmium were prioritised among chemical contaminants due to their high-risk levels, particularly for vulnerable populations such as children and pregnant women. A Quantitative Microbial Risk Assessment (QMRA) model was then applied to explore the impact of variables such as storage temperature, pasteurisation, and consumption practices on microbial risk across four dairy products: milk, cheese, butter, and cream. The baseline risk of E. coli in pasteurised milk was estimated at 2.35 × 10⁻¹², with improper refrigeration shown to significantly increase risk. At the same time, domestic storage conditions associated with climate change were found to elevate the risk of Listeria by up to 30%. In parallel, chemical risk assessments using probabilistic modelling indicated that aflatoxin B1 poses the most serious concern, especially in relation to contaminated animal feed. Nitrates and nitrites, in contrast, exhibited lower risk levels with Margin of Exposure (MOE) values above EFSA’s safe thresholds. These findings were used to inform the development of CheMiRisk, a novel decision support system that integrates microbial and chemical risk data with climate scenario modelling. CheMiRisk was validated with over 90% predictive accuracy and includes features that allow for scenario testing and mitigation strategy evaluation, supporting industry stakeholders and regulators in proactive decision-making. A particular strength of this research lies in its integration of population-specific risk assessments, accounting for the disproportionate burden of exposure faced by sensitive groups. The study also demonstrates how climate-related disruptions in the cold chain, particularly at the domestic level, may influence microbial proliferation and overall food safety. In conclusion, the thesis provides a comprehensive and flexible risk assessment framework that enhances the current state of food safety science. Combining open data, predictive modelling, and climate-informed scenario analysis. This work offers a practical framework for addressing emerging risks in dairy food safety and managing the evolving challenges of microbial and chemical contamination in dairy products, offering valuable guidance for future policy and regulatory strategies.2026-05-18 JG: Author's and/or other hand signatures removed for GDPR complianc