Training in metataxonomics-integrated risk assessment for foodborne pathogens in the Polish and Spanish dairy chain...

Food safety is a key concern in the European Union, with the harmonisation of risk assessment methodologies being a strategic priority. The EU-FORA programme, coordinated by EFSA, promotes standardised approaches to microbial risk assessment across Europe. Metagenomic sequencing has advanced the understanding of microbial ecosystems in food production, with Illumina (short-reads) and Oxford Nanopore Technologies (ONT) (long-reads) playing significant roles in detecting pathogens and characterising microbial communities. These technologies differ in accuracy, read length and resolution, potentially influencing risk profiles when used in quantitative microbiological risk assessment (QMRA). This fellowship, conducted at UPCT in Spain and IBPRS-PIB in Poland, compares the two platforms in assessing microbial populations in Polish and Spanish dairy chains. It explores how sequencing strategy affects hazard identification and QMRA outcomes, while also demonstrating how metagenomic data can enhance predictive modelling and support practical improvements in food safety management.