Whole genome sequencing in AMR surveillance

Introduction

Whole genome sequencing (WGS) is a comprehensive method used to determine the complete DNA sequence of an organism’s genome. As the cost of WGS continues to decrease, more laboratories and governments are considering whether to introduce it for applications such as antimicrobial resistance (AMR) surveillance. In this course, you will be introduced to the basics of WGS and how it can be applied to AMR surveillance efforts in your country or region.

After completing this course, you will be able to:

  • describe the basic principles of WGS
  • explain when, how and why WGS is used in AMR surveillance, and how it complements other types of testing and data to strengthen the AMR surveillance system
  • give examples of how WGS is used in AMR-related surveillance
  • reflect on how increasing WGS capacity could strengthen AMR surveillance in your work
  • recognise the cost and economic advantages of WGS for AMR surveillance and understand the barriers to its implementation
  • outline what is needed to make the case for increasing WGS capacity in your work.

In order to achieve your digital badge and Statement of Participation for this course, you must:

  • click on every page of the course
  • pass the end-of-course quiz
  • complete the course satisfaction survey.

The quiz allows up to three attempts at each question. A passing grade is 50% or more.

When you have successfully achieved the completion criteria listed above you will receive an email notification that your badge and Statement of Participation have been awarded. (Please note that it can take up to 24 hours for these to be issued.)

Activity 1: Assessing your skills and knowledge

Timing: Allow about 10 minutes

Before you begin this course, you should take a moment to think about the learning outcomes and how confident you feel about your knowledge and skills in these areas. Don’t worry if you do not feel very confident in some skills – they may be areas that you are hoping to develop by studying these courses.

Now use the interactive tool to rate your confidence in these areas using the following scale:

  • 5 Very confident
  • 4 Confident
  • 3 Neither confident nor not confident
  • 2 Not very confident
  • 1 Not at all confident

This is for you to reflect on your own knowledge and skills you already have.

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1 What is whole genome sequencing and how can it be used for AMR surveillance?