Introduction to Whole Genome Sequencing (WGS) in AMR surveillance​

The course originally ran over 6 days in February 2021, starting Monday 15 February, and ending Friday 26 February 2021.

​Recordings and Course material

This course is now freely available for self-learning. Presentations, Zoom recordings from the original course and course material to conduct the exercises have been combined and are available through the PDF file found below.

Please ​note that since this course is self-learning, we are not able to provide feedback on work submitted for the exercises beyond the automated response to certain questions.

Start your self learning here:

   Course material

Disclaimer: ​The course material is not be used for commercial purposes.

Please also note that the rapid development of sequencing technology might cause

certain information to be incomplete.

Course information

Title: Introduction to Whole Genome Sequencing (WGS) in Antimicrobial Resistance (AMR).

Language of instruction: English.

Offered as: Webinar with lectures, exercises and panel discussion.

Duration of course: 6 x ½ days.

Responsible: Rene S. Hendriksen (DTU),

Course co-responsible: Pernille Nilsson (DTU), Anthony Smith (NICD, South Africa), Jinal Bhiman (NICD, South Africa), Marco van Zwetselaar (KCRI, Tanzania), Beverly Eygir (NMIMR, Ghana), Iruka N. Okeke (UI, Nigeria).

General course objectives:

The course provides an introduction to Whole Genome Sequencing (WGS) and its use in Antimicrobial resistance (AMR) surveillance.

The participant will upon completion of the course i) know what WGS is and how it can be used and ii) be able to use freely available online tools to perform simple bioinformatics analysis and interpret results.

Learning objectives:

A participant who has met the objectives of the course will be able to:

  • ​Describe the potential uses of WGS in public health microbiology
  • ​Describe the different sequencing platforms and the technology behind using the correct terminology
  • ​Plan sampling/surveillance appropriate for with WGS studies with epidemiology in mind
  • Perform drag-and-drop bioinformatics using online analysis tools and interpret the results


The course covers sampling strategies for doing WGS in AMR, sequencing terminology, detailing state-of-the art technology including technical specifics of whole genome sequencing to give the participants a thorough understanding. Furthermore the course covers what the output data looks like, the importance of quality control and the use of online tools to analyse the data for species identification and AMR detection.

The course will comprise of lectures and hands-on exercises that the participants will have to complete and submit answers to in between course days.

Course literature:

No literature required.


None and novel users.

Material and Agenda from original course in 2021​

Course material

(PDF document)​​

Links to videos

Video 1 The present and future in AMR suveillance - Rene S. Hendriksen

Video 2 Application of WGS in public health microbiology - Rene S. Hendriksen

Video3 Taking epidemiology into account - what to sequence and how much - Alessandro Foddai

Video 4 Overview of terminology and different sequencing platforms: Illumina, Ion Torrent, Pacific Biosciences (PacBio), Oxford Nanopore Technologies - Jette Sejer Kjeldgaard

Video 5 Basic quality control of raw reads - Mushal Allam

Video 6 Bioinformatics Basics - Marco van Zwetselaar

Video 7 Introduction to online tools - Stanford Kwenda

Video 8 Online tools 2 - Sonda Tolbert

Video 9 Online tools 3 - Anthony Smith

Video 10 Phylogeny - Construction, visualization and interpretation - Erkison Odih

Video 11 Genotype to Phenotype: Prediction of AMR by WGS - Jette Sejer Kjeldgaard

Video 12 The Nagoya protocol: An introduction Carolina dos Santos Ribeiro

Video 13_1 Genomic surveillance NICD - Anthony Smith

Video 13_2 Genomic and metagenomics based surveillance of AMR in the United States under the National Antimicrobial Resistance Monitoring System (NARMS) - Errol Strain

Video 13_3 WGS surveillance in Europe - Rene Hendriksen

Video 13_5 Integrated surveillance of AMR and the ESBL Ec Tricycle project - Jorge Matheu

Evaluation Survey

Please evaluate the course through this link:​ Introduction to WGS in AMR surveillance Evaluation


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