MLST

Overview

Teaching: 10 min
Exercises: 30 min

Questions

• How can we detect the MLST type

Objectives

• What is MLST?

• Detect the MLST type

• Compare with results from other groups

MLST

Now that we have assembled our genome we are going to determine the MLST type. We are going to use a loop to cycle through the files. This is handy if you have multiple files to process.

Running it to display it on a screen:

$ mlst --list #check if there is an ecoli scheme (there are two, ecoli_achtman_4 is the correct one). 
$ cd ~/assembly
$ for sample in barcode02 barcode03
> do
>  mlst $sample/assembly.fasta
> done

The output of the mlst contains many lines as it checks for every possible species. You can specify an MLST scheme using the –scheme option and you can make it less chatty using the –quiet option. You can also store the actual MLST output in a file and only display the rest of the diagnostic messages on a screen.

$ cd ~/assembly
$ for sample in barcode02 barcode03
> do
>  mlst $sample/assembly.fasta
> done > mlst_output.txt
$ cat mlst_output.txt

Add the MLST sequence type to the Google sheet.

Challenge: Why are some MLST types not found. Compare with your classmates Are they still the same strain?

Find out what the allele differences are. If there are new alleles, try to get the novel allele sequences.

Hint:

$ run mlst --help for a hint

Solution

$ cd ~/assembly/barcode02/
$ mlst --scheme ecoli_achtman_4 --novel novel_alleles.txt assembly.fasta
 

Do you have novel alleles? what could be the reason? Compare with your sequence coverage. Why is it good to run specifically the E. coli scheme? what happens if you don’t?

Key Points

• Multi Locus Sequence Typing can be used to track strains

• MLST resolution is not very high but it is still useful

• Sequence errors can lead to incomplete MLST types