ClonalTracker: a tool to elucidate dissemination patterns between vancomycin-resistant Enterococcus faecium isolates

The global spread of vancomycin-resistant Enterococcus faecium (VRE), which commonly occurs in hospital environments, has become a major public health concern. To facilitate genomic surveillance and tracking the transmission of VRE, ClonalTracker was designed. This tool assesses the clonal relatedness between two VRE isolates given the respective assembled genomes by analyzing the van operon, the respective transposon type and the whole genome similarity. ClonalTracker has been validated using two previously analyzed publicly available datasets and I showcase its applicability on a yet unprocessed third dataset. While the method agrees with previously published results, it is able to provide more resolution at the clustering level even in the absence of plasmid information and using as reference the minimal version of the vancomycin resistance transposon. Within this third dataset composed of 323 vanB VRE isolates, ClonalTracker found that clonal expansion is the most common dissemination mode. All in all, this tool provides new bioinformatic means to uncover dissemination patterns and elucidate links between vancomycin-resistance isolates and can be broadly accessible via its webserver hosted at www.clonaltracker.nl (as of January 2024). The local version of this tool is also available at: https://github.com/victoriapascal/clonaltracker