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Finding antibiotic-resistant genes

In this tutorial we will find antibiotic-resistant genes in a bacterial genome.

New to Galaxy? First try the introduction and then learn some key tasks

Get data

  • Log in to your Galaxy instance (for example, Galaxy Australia, usegalaxy.org.au).

Use shared data

If you are using Galaxy Australia, you can import the data from a shared data library.

In the top menu bar, go to Shared Data.

  • Click on Data Libraries.
  • Click on Galaxy Australia Training Material: Annotation: Microbial Annotation.
  • Tick the box next to the file.
  • Click the To History button, select As Datasets.
  • Name a new history and click Import.
  • In the top menu bar, click Analyze Data.
  • You should now have one file in your current history.

Or, import from the web

Only follow this step if unable to load the data files from shared data, as described above.

  • In a new browser tab, go to this webpage:

DOI

  • Find the file called contigs.fasta
  • Right click on file name: select “copy link address”
  • In Galaxy, go to Get Data -> Upload File
  • Click Paste/Fetch data
  • A box will appear: paste in link address
  • Click Start
  • Click Close
  • The file will now appear in the top of your history panel. When it has finished uploading, the file name will be green.

Shorten file name

  • Click on the pencil icon next to the file name.
  • In the centre Galaxy panel, click in the box under Name
  • Shorten the file name.
  • Then click Save

Find antibiotic-resistant genes

We will use the tool called ABRicate to find antibiotic-resistant genes in the (draft) genome.

In the tools panel seach box, type in “abricate”

  • Click on ABRicate
  • For Input 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 have used a miniature genome in this example, so only have a few rows).

  • This shows a table with one line for each antibiotic-resistant gene found, in which contig, at which position, and the % coverage.

abricate results

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).

See this history in Galaxy

If you want to see this Galaxy history without performing the steps above:

  • Log in to Galaxy Australia: https://usegalaxy.org.au/
  • Go to Shared Data
  • Click Histories
  • Click Completed-Abricate-analysis
  • Click Import (at the top right corner)
  • The analysis should now be showing as your current history.

What’s next?

To use the tutorials on this website:

  • ← see the list in the left hand panel
  • ↖ or, click the menu button (three horizontal bars) in the top left of the page

You can find more tutorials at the Galaxy Training Network: