Wyres lab

Kaptive is a tool for identification of bacterial surface polysaccharide synthesis loci from genome assemblies. It was originally developed for application to capsule and LPS loci in Klebsiella pneumoniae and closely related species (see papers here and here). Additional databases have since been developed for Acinetobacter baumanii (in collaboration with Johanna Kenyon, Griffith University) and Vibrio parahaemolyticus (third party database). Kaptive is implemented in the Pathogen.watch global surveillance platform and Kaptive Web for ease of use. Ongoing development of Kaptive is led by the Wyres lab, in collaboration with the Holt lab. Major contributors have included Ryan Wick, Margaret Lam, Thomas Stanton and Kat Holt.

Bactabolize is a tool for rapid generation of strain-specific genome-scale metabolic models and growth phenotype predictions. It uses a reference-based approach to generate models from genome assemblies as described here. It can predict growth outcomes for a range of media conditions in aerobic or anaerobic atmosphere, as well as the impact of single gene deletions. Bactabolize was developed in the Wyres lab by Ben Vezina, Helena Cooper and Kelly Wyres, in collaboration with Stephen Watts (University of Melbourne) and Jane Hawkey (Monash University).

A Bactabolize-compatible curated pan-metabolism reference model for the K. pneumoniae species complex is available here.

Kleborate is a tool for rapid genotyping of K. pneumoniae and closely related species in the K. pneumoniae species complex (KpSC). It performs 7-gene multi-locus sequence typing, and characterises virulence and antimicrobial resistance determinants focussing only on determinants shown to be relevant for the KpSC (see this paper for details). Like Kaptive, Kleborate is available in Pathogen.watch for ease of use. It is also accompanied by Kleborate-viz, an interactive web application for visualisation and exploration of Kleborate results. Kelly is a co-developer of Kleborate alongside Margaret Lam, Ryan Wick and Kathryn Holt; ongoing development is led by the Holt lab.