GenEpi-BioTrain - Virtual training 01: Whole-genome sequencing-based (WGS) detection of antimicrobial resistance (AMR) in bacteria

Topic outline

• Whole-genome sequence-based detection of antimicrobial resistance in bacteria (GenEpi-BioTrain - Virtual training 1)

  Whole-genome sequence-based detection of antimicrobial resistance in bacteria (GenEpi-BioTrain - Virtual training 1)

  Welcome to this virtual training space on EVA.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. Explore the materials available 

  2. Install the software indicated below

  3. Suggest topics of interest for future virtual trainings.
  

  • ForumAnnouncements
• Aim and Objectives

  Aim and Objectives

  Aim

  The aim of this virtual training is to introduce participants to theoretical and practical aspects of detection of antimicrobial resistance (AMR) in bacteria using whole-genome sequence (WGS) data.

  Intended learning outcomes

  Upon completion of this workshop, participants will be able to:

  ·       Describe available open-source tools for detection of AMR in WGS data

  ·       Describe the impact of different sequencing technologies on the detection of AMR

  ·       Evaluate the advantages and disadvantages of AMR prediction based on phenotypic and genotypic methods in the context of surveillance

  ·       Critically evaluate the results of bioinformatics tools for detection of AMR in WGS data

  ·       Troubleshoot in case of discordance between the results of different bioinformatics tools

  ·       Troubleshoot in case of discordance between AMR genotype and phenotype in Enterobacterales, Staphylococcus aureus and Enterococcus sp.
• Format and Structure

  Format and Structure

  Format

  This virtual training takes place over two sessions that will be held on 4 and 8 September 2023, from 12:30-16:00. Participants will be assigned some exercises to conduct in between the two online sessions.

  Outline

  Session 1: Introduction to AMR in bacteria and software tools to detect AMR in WGS data.

  Session 2: Interpretation and reporting of results obtained using different software tools.
• Software requirements

  Software requirements

  For the training, participants will use the following open-source tools for detection of AMR:
  

  ·       AMRFinderPlus

  ·       CARD

  ·       PathogenWatch/Kleborate

  ·       ResFinder

  Some of these tools are available both as web-interface and as downloadable version to install locally. Participants who can install and operate the software tools locally are encouraged to do so.
• Session 1 (4 September): Introduction to AMR in bacteria and software tools to detect AMR in WGS data

  Session 1 (4 September): Introduction to AMR in bacteria and software tools to detect AMR in WGS data
  
  

  • Recorded session

  • S1 - Click the check-box after you watch the video

    
    

    
    

  • FileSession 1 - Presentation
  • FileSession 1 - Slido poll-results
  • FileSession 1 - Resources and further reading
• Practical exercise

  Practical exercise
  • FileStage 1 - Instructions
  • FileStage 2 - Instructions
  • FolderStage 2 - WGS data
• Session 2 (8 September): Interpretation and reporting of results obtained using different software tools

  Session 2 (8 September): Interpretation and reporting of results obtained using different software tools

  

  • Recorded session

  • S2 - Click the check-box after you watch the video

    
    

    
    

  • FileSession 2 - Presentation
  • FileSession 2 - Slido poll-results
• Contacts

  Contacts

  For any questions regarding the this virtual training, please use the discussion forum.

  If you have questions about the GenEpi-BioTrain programme, please address ECDC.Microbiology@ecdc.europa.eu.

  If you have questions regarding other training initiatives please contact: Courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Front Office FrontOffice@ecdc.europa.eu.