The rapid growth of advanced molecular methods has revolutionized our understanding of epidemiology of infectious diseases. This course will introduce you to basic molecular typing tools, but also to next-generation sequencing and will illustrate applications of these tools in epidemiological studies. In this course, you will work with whole genome sequences, learn about sequence alignment and construct phylogenies. You will get an introduction to coalescent theory and see examples of the use of molecular epidemiology in outbreak analyses. Examples of genome-wide association studies and microbiome studies will be presented. The application of mathematical modelling of pathogen evolution and epidemiology will be discussed.

At the end of this course, participants will

• Understand the molecular basis of comparative and universal strain typing methods
• Be able to construct and interpret simple phylogenetic trees
• Appreciate the value and limitations of molecular methods in demonstration of causal associations and direction of pathogen transmission
• Understand the value of the application of molecular data in mathematical modelling of infectious diseases
• Know the basics of coalescent theory and the use of molecular data in outbreak analysis
• Have seen examples of genome-wide association studies and epidemiological studies regarding the microbiome
• Understand the basic concepts of mathematical models of pathogen evolution and epidemiology