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Course Description

With increasing adoption of high-throughput sequencing technologies to infectious disease surveillance and outbreak investigations, genomic epidemiology (combining pathogen genomics data with epidemiological investigations to track the spread of infectious diseases) is poised to change the practices of public health and infection controls and provides unprecedented amount of data for pathogen evolution studies.

This 4-day course from CBW provides an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools or access to publicly available web applications.

Course Objectives

Participants will gain practical experience and skills to be able to:

  • Understand high-throughput sequencing (HTS) platforms as applied to pathogen genomics and metagenomics sequencing
  • Understand the value of data sharing and data curation in pathogen surveillance
  • Analyze HTS data for pathogen surveillance and outbreak investigations
  • Analyze antimicrobial resistance genes
  • Detect emerging pathogens in metagenomics data
  • Perform phylodynamic analysis
  • Use different visualization tools for genomic epidemiology analysis
Target Audience

Graduates, postgraduates, staff bioinformaticians, laboratory technologists, medical microbiologists and PIs working with or about to embark on analysis of genomic and metagenomics data for epidemiological investigations. Open to all public health, hospitals, academia, industry or government affiliations.


You will require your own laptop computer. Minimum requirements: 1024×768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).

This workshop requires participants to complete pre-workshop tasks and readings.

Course Outline

Module 1: Introduction to Public Health Microbiology and Genomic Epidemiology (Will Hsiao)

  • Review of relevant terms and concepts
  • Review of next generation sequencing and its application to microbiology
  • Overview of sequence data processing
  • The importance of metadata quality and curation
  • Overview of different types of genomic epidemiology analysis
  • Computing Resources and Requirements 

Module 2: Phylogenetic Analysis (Fiona Brinkman)

  • Overview of microbial evolution
  • Overview of population genetics of pathogens
  • Review of phylogenetics

Module 3: Data Curation and Data Sharing (Emma Griffiths)

  • Overview of data sharing platforms for pathogen surveillance data
  • Importance of data curation to facilitate data sharing efforts
  • Best practices in data curation and data sharing

Lab Practical: Hands on exercise to curate data to private and public repositories in standardized formats. Best practices for submission.

Module 4: Viral Pathogen Genomic Analysis -Single Nucleotide Variants (Jared Simpson)

  • Overview of single-nucleotide-variants (SNVs)
  • Whole genome SNVs analysis of viral pathogens using HTS data
  • Reference-based vs. Reference-free SNVs analysis
  • Advantages and complications associated with SNVs analysis
  • Integration of epidemiological data for SNVs analysis

Lab Practical: 

  • Run an HTS analysis workflow to generate a virus consensus genome and variant calls
  • Perform quality control on the HTS data and workflow results
  • Building and interpreting viral phylogenetic trees using SNVs
  • Visualization of analytical results

Module 5: Bacterial Pathogen Genomic Analysis (Ed Taboada) 

  • SNVs analysis of bacterial pathogens
  • Overview of Multi-locus Sequence Typing (MLST) and Whole-Genome or Core-Genome (WG/CG) -MLST analysis
  • Concept of Nomenclature database and global surveillance
  • Bacterial typing
  • Publicly available MLST and WG/CG-MLST databases
  • Assembly-based vs. Assembly-free MLST analysis
  • Integration of epidemiological data for MLST analysis

Lab Practical: 

  • Building and interpreting bacterial phylogenetic trees using SNVs
  • Building and interpreting Cladograms and Molecular Typing using WG/CG-MLST
  • Visualization of analytical results

Module 6: Antimicrobial Resistant Gene (AMR) Analysis (Andrew McArthur)

  • Review of available antimicrobial resistant (AMR) resources
  • The Comprehensive Antimicrobial Resistance Database (CARD) Overview
  • Annotation of AMR using ResFams and Active Sites annotation
  • Identification of antimicrobial resistance genes 
  • Challenges of Detecting AMR in Metagenomics 

Lab Practical: 

  • Using CARD website
  • Using Resistance Gene Identifier (RGI) and other bioinformatics tools to identify and characterize AMR genes

Module 7: Phylodynamics and Transmission Analysis (Finlay Maguire)

  • Overview of phylodynamics
  • Inferring epidemiological parameters
  • Reconstructing transmission networks

Lab Practical: 

  • Phylodynamic analysis using SARS-CoV-2 genomes
  • Inference of infectious disease transmission networks from genomes 

Module 8: Emerging Pathogen Detection and Identification (Aaron Petkau)

  • Overview of Pathogen Identification using metagenomics
  • Bioinformatics tools for pathogen detection and identification
  • Identify reference datasets or databases suitable for pathogen detection

Lab Practical: Identification and characterization of an emerging pathogen using sequence data

Module 9: Mobile Genetic Elements and Environmental Microbiome (Gary Van Domselaar)

  • Using environmental samples for pathogen surveillance (e.g. waste water)
  • Impact of horizontal gene transfer and analysis of microbiome
  • Bioinformatics tools for pathogen detection and identification

Lab Practical: Using the ARETE pipeline to process and annotate environmental microbiome samples for pathogen analysis

Workshop Details:

Duration: 4 days

Start: Apr 18, 2023

End: Apr 21, 2023

Course Mode:

Status: Registration Closed

Workshop Ended

CAD $100 for applications received between February 1, 2023 to March 18, 2023
CAD $200 for applications received between March 19, 2023 to April 4, 2023
Limited to: 40 participants
Open Access Content:

Canadian Bioinformatics Workshops promotes open access. Past workshop content is available under a Creative Commons License.


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