v3.0.0

Kleborate v3 is a major a rewrite of the Kleborate v2 code base.

It aims to:

• Modularise the code for easier extensibility and maintenance
• Provide functionality for other species, e.g. Klebsiella oxytoca species complex and Escherichia coli
• Replace the BLAST dependency with minimap2

When Kleborate v3 is run using the -p kpsc option to run preset modules for K. pneumoniae the same logic is implemented as Kleborate v2, plus the following changes/updates:

• MLST & virulence databases updated (April 2024)
• Column Chr_ST has been removed in v3, as it is redundant with ST
• AMR database updated based on CARD v3.2.9 (June 2024)
• Added $ to indicate when PmrB or MgrB have a mutation in the start codon that may disrupt translation (in Col_mutations column)
• Added check for synonymous mutation in ompK36 (25 C > T) associated with increased resistance to carbapenems (in Omp_mutations column)
• Updated to use Kaptive v3, which has some changes to the names of output variables:
  • K_locus_missing_genes has been renamed K_Missing_expected_genes
  • O_locus_missing_genes has been renamed O_Missing_expected_genes
  • New columns are included in Kleborate v3: K_Coverage , O_Coverage

New modules have been added to perform MLST for Klebsiella oxytoca species complex and Escherichia coli
Additional modules for these and other species are in development and will appear in future releases.

Major contributors:

• Ryan Wick (designing the modular framework and transitioning some functions to modules)
• Mary Maranga (refining modular framework and logic, developing and testing new modules, developing documentation)
• Tom Stanton (minimap logic and Kaptive integration)
• Margaret Lam, Kara Tsang (database updates and testing)