A tool to assess the relatedness between any two given VRE isolates

A bit of background...

The rise of reported vancomycin-resistant Enterococcus faecium (VRE) infections worldwide highlights the importance of detecting outbreaks in a timely fashion. Whole-genome sequencing data can be useful to understand dissemination modes of vancomycin-resistant genes. For this reason, we have built ClonalTracker to compare any two VRE genomes. The ClonalTracker can be used from the command line but we have also designed the web server so that any researcher with or without bioinformatic experience can use it.

How to run ClonalTracker

Input files

ClonalTracker uses as input two assembly files in FASTA format for any two given VRE isolates. It is important to note that the quality of the assembly directly influences the tool performance as it depends on how (well) the van-containing transposon is reconstructed. Also, be aware that using genomes assembled with different tools might interfere with the end result.

Important note: the accuracy of the results directly depend on the quality of the inputted assemblies. Please, assess the contiguity, completeness, and correctness of your assembly files. You can read more on how to assess the quality of genome assemblies here. For guidance, 124 assemblies have been used to test ClonalTracker with a mean N50 value of 43.86 and an N75 of 22.88.


1. van-typing using Blastn

BLAST (basic local alignment search tool) is an algorithm that aligns any given sequence (query) to a database of nucleotide sequences in this case. The database ClonalTracker uses is composed of 6 different van operons including vanA and vanB type. As query, ClonalTracker uses all the contigs/scaffolds available from the isolate's assemblies. The van type is assigned based on the highest similarity hit, if the isolate is vancomycin-resistant. The next step will be performed only when the two isolates are of the same van type. You can read more about BLAST here.

2. Transposon-typing using Blastn, ISEScan, RagTag, Clinker and Blastn

3. Whole genome comparison with PopPUNK and Mash