Introduction to Genomic Epidemiology of Infectious Diseases


This course will provide an intensive introduction to the methods used for analysis of whole genome sequencing (WGS) data and its application to infectious disease  epidemiology. Students will learn bioinformatics approaches to WGS analysis through a combination of lectures and hands-on workshops. Topics will include how to perform de novo versus reference-based assembly, how to identify (‘call’) single nucleotide polymorphisms, and creating/interpreting phylogenetic trees. Emphasis  will be placed on applications of WGS to outbreak investigation, study design issues and minimizing bias in genomic epidemiologic studies, and the implications that  these data can have for public health. While command line may be used during this course, a priori knowledge is not required.



2017 Agenda Introduction to Genomic Epidemiology of Infectious Diseases


Course Directors

Marcel Behr, MD, MSc
Director, McGill International TB Centre
Professor of Medicine, McGill University
Microbiologist-in-Chief, McGill University Health Centre
Robyn Lee, PhD
Research Fellow, Department of Microbiology and Immunology, University of Melbourne
The Microbiological Diagnostic Unit Public Health Laboratory
The Peter Doherty Institute for Infection and Immunity
Erwin Schurr, PhD
Professor, McGill University
Leader, Infectious Diseases and Immunity in Global Health Program,
Research Institute of the McGill University Health Centre


Course Faculty

Vanessa Allen, MD MPH – Public Health Ontario
Marcel Behr, MD MSc – McGill University
Ken Dewar, PhD – McGill University
Vinicius Fava, PhD – McGill University
Jennifer Gardy, PhD – British Columbia Centre for Disease Control

Anders Goncalves da Silva, PhD – The University of Melbourne

Robyn Lee, PhD – The University of Melbourne

Ines Levade, PhD(c) – Université de Montréal

Greg Matlashewski, PhD – McGill University

Erwin Schurr, PhD – McGill University
Torsten Seemann, PhD – The University of Melbourne
B. Jesse Shapiro, PhD – University of Montreal




This course will introduce the basic principles of genomic epidemiology of infectious diseases. Lectures will cover the methodology behind key WGS analyses and  phylogenetic approaches, as well as study design considerations for genomic epidemiology. Lectures will also provide concrete examples of the application of WGS to investigate infectious disease transmission, both in public health and research contexts. Morning sessions will commence with lectures, followed by students  breaking into small groups where they discuss published genomic epidemiology manuscripts (provided in advance). The aim of these small groups is to help  students learn to critically appraise genomic epidemiology papers, and discuss aspects such as study design and analytic approaches used to address the research  questions therein. Afternoon sessions will similarly commence with lectures, followed by practical, hands-on data analysis workshops where students will learn to  complete various aspects of WGS data analysis. Time will also be allocated throughout the course for students to ask questions and receive advice on their own WGS  analysis and/or research projects. Participants are encouraged to bring their laptops. Mac or Linux-based is preferred; however, Windows-based PCs are accepted.



Target audience

  • Epidemiologists and Laboratory personnel from Public Health Units
  • Postdoctoral Fellows and Graduate students working on infectious diseases epidemiological research projects
  • Junior faculty with an interest in infectious diseases epidemiology research




Maximum of 40 participants.