Resistance genes

Overview

Teaching: 10 min
Exercises: 40 min

Questions

• How can we detect the resistance genes and point mutations

Objectives

• Finding resistance genes

• Finding mutations that cause resistance

• Compare with results from other groups

ResFinder

ResFinder is often used to find resistance genes and mutations. The output is human readable. Now that we have assembled our genome we are going to determine which resistance genes and point mutations there are. We are going to use a loop to cycle through the files. This is handy if you have multiple files to process. Resfinder is written in Python, so it must be run through that interpreter. It is often installed in its own conda environment because of it’s very specific dependencies. We run it with the option –acquired for the resistance genes and –point for the resistance point mutations. Please do not forget to activate resfinder.

$ conda activate resfinder
$ cd ~/assembly
$ for sample in barcode02 barcode03
> do
>  python -m resfinder  -s "Escherichia coli" --point  --acquired -ifa  $sample/assembly.fasta -o $sample/resfinder
> done
$ cd barcode02
$ ls
$ cd resfinder
$ ls
$ less -S pheno_table.txt
$ less -S ResFinder_results_table.txt
$ less -S PointFinder_table.txt
$ conda deactivate
$ conda activate base

The advantage of ResFinder is that it shows the phenotype associated with the resistance gene or mutations. It also shows the location of the resistance genes. The drawback is that is does not show on which contig the resistance causing point mutations are located.

AMRFinderPlus

AMRFinderPlus is also used to find resistance genes and mutations. The output is in the form of a table. It is often installed in its own conda environment

$ cd ~/assembly
$ conda activate amrfinder
$ amrfinder --list_organisms
$ for sample in barcode02 barcode03
> do
>  amrfinder --organism Escherichia --nucleotide $sample/assembly.fasta > $sample/amrfinderplus.txt
> done
$ conda deactivate
$ conda activate base
$ cd barcode02
$ ls
$ cat amrfinderplus.txt

Add the number of resistance genes to the Google sheet.

Challenge: Are the resistance genes found on a plasmid or on a chromosome?

Find out where the genes are located. Pick a resistance gene or point mutation, and see if you can figure out if it is on the chromosome or on a plasmid. Remember the assembly info file, the sequence graph analysis etc.

Hint: Which contig is it on

Solution

Investigate the assembly graph using Bandage. Was it on a smaller circular contig or a large 5 megabase contig?

Where are the genes and where are the point mutations? Add it to the Google sheet.

Key Points

• Resistance genes can be found on the chromosome and on plasmids

• Point mutations are often in essential chromosomal genes

• The translation from resistance genotype to phenotype is not always easy