The course aims to provide students with the theoretical foundations and practical skills needed to analyze evolutionary and epidemiological processes, both in broader terms and with a specific focus on pathogenic microorganisms. By the end of the lessons, students will have gained familiarity with the main methods used in genomic epidemiology and will be able to employ them to map pathogen characteristics and track outbreak dynamics starting from genomic sequencing data.
Prerequisiti
To successfully attend the course, a basic knowledge of the fundamental concepts of genetics, molecular biology, and evolution is necessary. Regarding the practical classes, preliminary skills in statistics and bioinformatics are also essential, including familiarity with the use of the command line interface.
Metodi didattici
The course will follow an integrated format, combining lectures and practical bioinformatics exercises. This approach will allow students to test the concepts learned in real time on case study datasets. At the end of each class, the presentations from both the lectures and practical sessions will be shared with the students via the university portal. The use of a personal laptop is mandatory for practical activities. Students will receive support from the teacher both during the installation phase of the required software and throughout the execution of the practical bioinformatics sessions.
Verifica Apprendimento
The final evaluation will consist of an oral examination that begins with the student presentation of a case study covered or agreed upon during the course. Following the presentation, the exam will continue with a series of questions designed to verify both basic theoretical concepts and the student's critical thinking skills when reasoning about the epidemiological scenarios discussed during the lessons. The overall final grade for the course will be calculated as an average of the two modules (GENOMICS AND EPIDEMIOLOGY OF INFECTIOUS DISEASES and COMPARATIVE GENOMICS AND METAGENOMICS IN VECTORS AND PATHOGENS).
Testi
preparation. For further reading, the following texts are recommended: 1) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Sequence Evolution. Marco Salemi, Philippe Lemey, Vandamme 2) Molecular Evolution: A Phylogenetic Approach. Ziheng Yang
Contenuti
The course addresses the study of infectious diseases by integrating the classic epidemiological approach with modern genomic analysis methodologies. The course will initially introduce the historical development of epidemiology and the evolution of public health surveillance systems. Subsequently, the different types of study designs and mathematical models used to describe and quantify the spread of pathogens within populations will be covered. The second part of the program will focus on the computational and evolutionary aspects, starting with the basics of phylogenetics and methods for reconstructing phylogenetic trees of viruses and bacteria. Finally, the core principles of genomic epidemiology will be illustrated, showing how next-generation sequencing (NGS) data enable the identification of transmission clusters, the tracing of outbreak origins, and the monitoring of variant spreads or drug resistances. Each topic will be paired with the analysis of case studies, allowing students to directly apply the learned concepts through practical exercises and the use of bioinformatic software.
