Our resources
We are proud to develop software and other resources that support the global research community.
Kaptive
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, 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 Thomas Stanton, Ryan Wick, Margaret Lam and Kat Holt.
Bactabolize
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).
KpSC-pan reference model
KpSC-pan is a highly curated pan-reference metabolic model for the K. pneumoniae Species Complex (K. pneumoniae and closely related taxa). The most recent version of KpSC pan (KpSC-pan-v2) captures the metabolism of more than 500 individual KpSC. It can be used with Bactabolize to generate KpSC strain-specific models with high accuracy.
KpSC-pan-v2 was curated and validated by Helena Cooper as part of her PhD project. Ongoing curation is led by Kalani Paranagama.
KlebNET Metadata Repository
The KlebNET Metadata Repository is an open source database housing contextual metadata for publicly available KpSC whole genome sequences. It includes information about the corresponding bacterial isolates, their hosts or environments, as well as the reasons they were sampled and sequenced. This type of information is essential to allow maximum use and reuse of publicly available genome data in research and surveillance studies.
Metadata collection is ongoing through a community effort as part of the KlebNET-GSP Epidemiology Consortium, coordinated by Kelly and Hina Salimuddin.
Kleborate
Kelly is also a contributor to Kleborate, 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. Ongoing development of Kleborate is led by the Holt lab.
Learning resources
- Kaptive tutorial– a step by step tutorial for installing and using Kaptive, and interpreting the outputs.
- Klebsiella pneumoniae Genomic Epidemiology and Antimicrobial Resistance lecture series– a set of lectures on KpSC population genomics and genomic surveillance tools. These were co-developed and delivered with colleagues from the KlebNET-GSP project as part of the ECDC Gen-Epi-Bio-train initiative. You can access the lecture slides here. The lecture recordings are available for free via the ECDC learning portal (you need to create a free account to access this).
- O polysaccharide nomenclature explainer– a blog post that walks through the most recent KpSC O polysaccharide nomenclature changes described in this review article.
Wyres lab 