Predicting pathogenic features (AMR, Virulence factors, Plasmids) (via Galaxy and the Web)

In this worksheet you will learn how predict a range of pathogenic features such as antimicrobial resistance and virulence factors (ABRicate), and plasmid presence (PlasmidFinder)
This is two separate analyses but use similar inputs

Required prerequisite(s)

You must create an account on https://usegalaxy.eu/ and log in to that account
You have uploaded the dataset files listed below to Galaxy by following one of the tutorials on the Loading data into Galaxy page

An understanding of how to use Galaxy. Some good guidance: https://www.youtube.com/watch?v=uVNdyrVDYYU
A knowledge of the two primary tools is useful. You can access their manuals here: ABRicate, PlasmidFinder

This demonstration uses the output of Assembling a genome from short reads (e.g. Illumina) using SPAdes worksheet but this will work on any assembly, such as that created in the Assembling a genome from long reads (e.g. ONT) using Flye worksheet. Thus, it is suggested you run at least one of these assembly methods first.
- You can download the example scaffolds output file of the SPAdes worksheet here: DRR187559_scaffolds.fasta

NOTE: ABRicate only looks for presence/absence of AMR-related genes and does not detect point mutations. To do this you should use the AbritAMR via UNIX worksheet

In your web browser, navigate to https://usegalaxy.eu/
Log in to your account using the ‘Login or Register’ button in the top navigation bar
Your datafile ‘DRR187559_scaffolds.fasta’ should already be in the history on the righthand side. If not, follow one of the tutorials on the Loading data into Galaxy page
In the lefthand side menu, in the search box under ‘Tools’ type abricate
Click on ‘ABRicate Mass screening of contigs for antimicrobial and virulence genes’
The ABRicate tool will now appear in the centre of the screen. This tool looks for genes in a genome file related to antimicrobial resistance or virulence.
Under ‘Input file (FASTA, Genbank or EMBL file’ make sure your genome is shown in the box (DRR187559_scaffolds.fasta in our case)
The default parameters for ABRicate are fine so you do not need to change anything if you so wish
ABRicate can take a while to run so it is suggested you click ‘yes’ under the ‘Email notification
Once done, click ‘Run Tool’
You will see the output files appear in your history on the right.
- Once these turn green and the clock symbol has disappeared the analysis is finished
To download any of these files click on the file in your history (righthand menu) and then click the small save icon that appears at the bottom left of that box.
- Most files can then be viewed in a text viewer such as Notepad++ or BBEdit
A description of what is contained in each output file can be found here

PlasmidFinder can be accessed via a webserver at https://cge.food.dtu.dk/services/PlasmidFinder-2.0/
First you must select the type of genome you have under ‘Select database’
- Since we have an MRSA sample we will select ‘Gram Positive’
The default identity and coverage percentage settings can be used so there is no need to change these
Under ‘Select type of your reads’ ensure that ‘Assembled or Draft Genome/Contigs’ is selected
Click the ‘Isolate File’ button and select the DRR187559_scaffolds.fasta file
Click ‘Upload’

Wait a few minutes for the analysis to finish. The screen will automatically move to the results when finished.

Get the information on contigs/scaffolds that may contain plasmids
- Be wary when interpreting these results and look carefully at the length of the plasmids (can view on NCBI website using the accessions listed at the end of each line)
- Often short hits (<1kb) can occur erroneously to plasmids on contigs with similar genes; this does not mean there is a plasmid there (or that a plasmid is not there if you get such short hits)
- Bad assemblies (i.e. large or messy assembly graphs in Bandage) can produce such results