Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

Licence: Creative Commons Attribution 4.0 International

Keywords: amr, bacteria, microgalaxy, one-health, microbiome

Authors: Bérénice Batut, Clea Siguret

Status: Active

Learning objectives:

Module: Species and contamination checking

  • Run tools to evaluate sequencing data on quality and quantity
  • Evaluate the output of quality control tools
  • Improve the quality of sequencing data
  • Run a series of tool to identify species in bacterial isolate sequencing data
  • Visualize the species abundance

Module: Assembly

  • Run tools to evaluate sequencing data on quality and quantity
  • Process the output of quality control tools
  • Improve the quality of sequencing data
  • Run a tool to assemble a bacterial genome using short reads
  • Run tools to assess the quality of an assembly
  • Understand the outputs of tools to assess the quality of an assembly
    • Run tools to evaluate sequencing data on quality and quantity
  • Process the output of quality control tools
  • Improve the quality of sequencing data
  • Run a tool to assemble a bacterial genome using short reads
  • Run tools to assess the quality of an assembly
  • Understand the outputs of tools to assess the quality of an assembly

Module: Genome annotation

  • Run a series of tool to annotate a draft bacterial genome for different types of genomic components
  • Evaluate the annotation
  • Process the outputs to formate them for visualization needs
  • Visualize a draft bacterial genome and its annotations

Module: AMR gene detection

  • Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
  • Get information about ARGs
  • Visualize the ARGs and plasmid genes in their genomic context

Recommended follow-up tutorials

  • Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
  • Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
  • Perform taxonomy profiling indicating and visualizing up to species level in the samples
  • Identify pathogens based on the found virulence factor gene products via assembly, identify strains and indicate all antimicrobial resistance genes in samples
  • Identify pathogens via SNP calling and build the consensus gemone of the samples
  • Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps

1

Module: Species and contamination checking

• beginner 1 material

Quality control and taxonomic assignation is useful in AMR detection to verify the quality of the data but also to check contamination and confirm species

Time estimation: 2 hours

3

Module: Genome annotation

• beginner 1 material

The generated contigs can be annotated to detect genes, potential plasmids, etc. This will help the AMR gene detection process, especially the verification and visualization

Time estimation: 3 hours

4

Module: AMR gene detection

• beginner 1 material

AMR gene content can be assessed from the contigs to detect known resistance mechanisms and potentially identify novel mechanisms.

Time estimation: 2 hours

Activity log