Module 3.3a - Pathogen-wave oriented analyses 2023 (outline)

Theme 3: Genome analysis and sharing

 

Genome analysis, AMR and outbreak detection

 

Time 

Activity description 

ILOs 

9.00-10.00

Lecture: “Introduction to genotypic detection of AMR”

  • General knowledge of Annotation and available annotation tools
  • Understand the principle of calling AMR genes
  • Understand genetic basis of AMR: acquired genes, mutations and intrinsic resistance
  • Awareness of available tools and databases: ResFinder, CARD, NCBI
  • Strengths and limitations of available databases
  • Species verification/identification 
  • Knowledge of k-mers and why we use them 
  • How to run tools and associated parameters

10.10-12.00

Practical: “Genotypic detection of AMR”. 

k-mer 

ResFinder 

PlasmidFinder 
  • Utilize available online and command line tools for identifying AMR genes and mutations 
  • Impact of sequence data format on results 
  • Interpretation of results 
  • Pitfalls and how to handle them

12.45-13.30

Lecture: “Introduction to bacterial typing of MRSA”
  • Methicillin-resistant Staphylococcus aureus 
  • Impact on public health 
  • Methods of typing MLST, spa typing and SCCmec typing
  • Virulence 

13.45-16

Practical: “Bacterial typing for use in public health”
  • What is multilocus sequence typing (MLST)  
  • High vs. low resolution surveillance methods 
  • How to do in silico: 
      - Identification of sequence type (ST)
      - spa typing
      - SCCmec typing
      - VirulenceFinder: virulence genes annotation
      - PlasmidFinder: plasmid replicons genes annotation
      - ResFinder: resistance genes annotation

 

Details

This module will introduce the participants to basic elements in use of WGS in outbreak analysis and surveillance of antimicrobial resistant pathogens. The module will contain two major parts: Firstly annotation of antimicrobial resistance determinants with use of available databases and secondly, introduction to typing of antimicrobial resistant bacteria, using methicillin resistant Staphylococcus aureus as an example.  The module will use a mix of lectures and practical hands on exercises.


Last modified: Monday, 25 March 2024, 11:19 AM