Workshop on Antimicrobial Resistance

3-7:30 PM London time (BST)
7-11:30 AM Vancouver time

A joint initiative with the Public Health Alliance for Genomic Epidemiology (PHA4GE) and the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), delivered on 15th October 2021.

Antimicrobial resistance is a global public health threat and this workshop aims to provide training on the following:

  • Use of existing AMR-related databases and resources (including CARD, NCBI, and PATRIC)
  • Theory and use of bioinformatics tools to detect AMR genes from genomes (e.g., AMRFinderPlus) 
  • How to compare and systematically report results from AMR genomics using hAMRonization
  • A practical introduction to bioinformatics workflows for AMR genomics

Programme and Material

Welcome and Introductions | Finlay Maguire, Emma Griffiths, Carolyn Johnson, Mark Pallen
Slides – PHA4GE introduction
Slides – JPIAMR introduction
Slides – CLIMB-BIG-DATA introduction

Introduction to databases and resources for AMR genomics | Kara Tsang (London School of Hygiene & Tropical Medicine, UK)

Overview of AMR gene prediction tools (including detection of variant-related AMR) | Mike Feldgarden (National Center for Biotechnology Information, USA)

Comparing and reporting AMR results using hAMRonization | Ines Mendes  (Instituto de Medicina Molecular, PT)

Practical demonstration: bacterial genomic reads to AMR gene reports | Finlay Maguire (Dalhousie University, CA)

Q/A – Panel Discussion | Video

Organising committee 

Andrew Page, Quadram Institute, UK, representing CLIMB-BD and PHA4GE
Emma Griffiths, SFU, Canada, representing PHA4GE
Mark Pallen, Quadram Institute, UK, representing CLIMB-BD
Lisa Marchioretto, Quadram Institute, UK, representing CLIMB-BD
Finlay Maguire, Dalhousie University, Canada, representing PHA4GE
Jessica Boname, MRC, UK, representing JPIAMR and MRC
Carolyn Johnson, MRC, UK, representing JPIAMR and MRC