Plasmid typing and classification

Overview

Teaching: 10 min
Exercises: 50 min

Questions

• How can we detect which contig is a plasmid and which is from the chromosome

Objectives

• Classifying plasmid contigs

• Typing plasmids

• Check which plasmids contain resistance genes

RFPlasmid

RFPlasmid is often used to classify contigs in plasmid and chromosome. RFPlasmid processes folders, therefore we don’t need a loop to process files.

$ cd ~/assembly
$ mkdir ~/assembly/genomes
$ cp ~/assembly/barcode02/assembly.fasta ~/assembly/genomes/barcode02.fasta
$ cp ~/assembly/barcode03/assembly.fasta ~/assembly/genomes/barcode03.fasta
$ cd ~/assembly
$ rfplasmid --specieslist
$ rfplasmid --jelly --species Enterobacteriaceae --input genomes --out rfplasmid
$ cd rfplasmid
$ cat prediction.csv

An alternative for RFPlasmid is Platon. It has very similar performance to RFPlasmid and is slightly more conservative. It can be run using the following commands:

$  platon assembly.fasta --output output --threads 2 --verbose --db /mnt/DGK_KLIF/open/db/platon/db

If you want to run a loop, please try the following:

$ cd ~/assembly
$ for sample in barcode17 barcode18 ; do platon $sample/assembly.fasta --output $sample/platon --threads 2 --verbose --db /mnt/DGK_KLIF/open/db/platon/db ; done

Please try it yourself. Try to find the output and open the files. Are there differences in the classification between RFPlasmid and Platon?

Plasmidtyping

It is useful to know which type of plasmids are present in your bacterial genome. We use Abricate and the PlasmidFinder database to find the Inc types or incompability groups. Abricate has different kinds of databases it can use to query a genome.

$ abricate --list # we check which databases are available. 
$ cd ~/assembly
$ for sample in barcode02 barcode03
> do
>  echo $sample
>  abricate --db plasmidfinder $sample/assembly.fasta
>  echo
> done

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 from the previous exercise, and see if you can figure out if it is on the chromosome or on a plasmid using this data. Also find out the incompability group of the plasmid (the PlasmidFinder Inc result).

Hint: Which contig is it on

Solution

Investigate the RfPlasmid or Platon classification of the contig. Is the resistance gene contig on a chromosomal or plasmid contig. Look up the contig name in the Abricate –db plasmidfinder output.

Can you try other Abricate databases? e.g. VFDB that checks for virulencefactors or ecoh that checks for E. coli serotype genes.

Key Points

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

• Plasmid classification by hand is time consuming. Especially with lots of contig, automated analysis is better

• There are also plasmids without resistance genes