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Finding antibiotic-resistant genes

Overview

  • Import an assembled bacterial genome
  • Find antibiotic-resistance (AMR) genes

Import data

  • Go to your Galaxy instance.

  • Set up a new History for this Activity.

    • In the History panel, click on the cog icon, select Create New.
    • A new empty history should appear; click on Unnamed history and re-name it (e.g. AMR genes).

    Galaxy new history

  • Import an assembled genome (or use one from your history).

    • Copy this URL for a previously-assembled genome: https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/SPAdes_contigs.fasta
    • From the Galaxy tool panel, click on Get Data → Upload File
    • Click the Paste/Fetch data button
    • Paste the URL into the box.
    • Click the Start button.
    • Once the progress bar reaches 100%, click the Close button
    • The file will now upload to your current history.
    • Re-name it with the pencil icon to contigs.fasta.

Find antibiotic-resistance genes

  • We will use the tool called ABRicate to find antibiotic resistance genes in the (draft) genome.
  • ABRicate uses a database of these genes called ResFinder.

In the tools panel, go to NGS Analysis: NGS Annotation: ABRicate.

  • For Select fasta file choose contigs.fasta (or the name of your own assembly file.)
  • Click Execute.

There is one output file. Click on the eye icon to view. It should look like this, although likely with a different number of rows. (We will probably only have a few rows as we have used a cut-down data set).

  • This shows a table with one line for each antibiotic resistance gene match in the database, in which contig, at which position, and the % coverage.
  • NOTE: The same gene might appear on multiple rows. Why might that be?

abricate results

Next

In the output from ABRicate, column 5 has the list of the antibiotic-resistant gene names. Some of these may be complete, exact matches, and some may have a gap/mutation in their sequence which can affect whether that protein is actually expressed.

To find out more about what type of AMR genes these are, you can search Genbank with the gene name (e.g. aadD).