94407 - Microbial Genomics For Risk Analysis In The Food Chain

Course Unit Page


This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.

Good health and well-being Responsible consumption and production Life on land

Academic Year 2021/2022

Learning outcomes

Students will acquire knowledges on microbial genomics applied to outbreak investigation, source attribution and risk assessment. Whole genome sequencing platforms and technologies will be described. Benefits of a real-time outbreak investigation and a more targeted source attribution and hazard identification/characterisation will be discussed along with major challenges and opportunities.

Course contents

• Whole genome sequencing platforms and technologies
• Introduction to microbial risk analysis
• WGS and outbreak investigation (definition of outbreak, subtyping approaches, platforms for real-time outbreak investigation)
• WGS and source attribution (frequency-matching, machine learning, network models)
• Genome Wide Association Studies and prediction of phenotypic traits
• WGS and risk assessment (pathogen typing and characterisation for hazard identification, prediction of virulence potential for dose-response relationships in hazard characterisation, prediction of phenotypic traits associated to growth/survival for exposure assessment)


Notes of lectures; scientific publications

Teaching methods

Oral lectures, scientific seminaries

Assessment methods

This course is part of the integrated subject "RISK ANALYSIS IN FOOD SAFETY AND ANIMAL WELFARE” which also includes "RISK ANALYSIS IN ANIMAL WELFARE ". Final grading of the entire integrated course is calculated as an average of the scores obtained in the two courses of " RISK ANALYSIS IN ANIMAL WELFARE " and "MICROBIAL GENOMICS FOR RISK ANALYSIS ". The examination commission includes teachers of both courses.
The oral examination will verify the theoretical and applicative knowledges of the student. Particularly positive will be evaluated the ability to move within the different topics and the achievement of an organic knowledge of the topics presented during the lessons.

Teaching tools

projector, computer

Office hours

See the website of Frederique Pasquali