v3.2.4

This release fixes issues with the checks for Flq_mutations in the Ciprofloxacin resistance prediction module.
Thanks to @karatsang.

v3.2.3

Two bug fixes in this release:

• Missing closing ] in the Ciprofloxacin_MIC_prediction column
• Issue [#105]

v3.2.2

This release fixes the headers of the E. coli AMR module.

v 3.2.0

This release includes the following updates:

• New AMR genotyping report for Kpsc, compatible with the hAMRonization standards
• Mutations are now reported using HGVS nomenclature
• Kara Tsang added a new module for Ciprofloxacin resistance prediction
• New modules for Escherichia species have been added, including: pathotyping, typing of the LEE pathogenicity island, Clermontyping, typing of stx types using StxTyper, O:H serotyping using ECTyper, AMR typing using AMRFinderPlus

v3.1.3

This release updates the MLST logic to account for the divergent iuc loci and fixes issue [#92]

Updated CARD DB to remove CatB4.v1 gene.

v3.1.2

This release fixes issues [#84 ] and [#88 ]

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)

v2.5

This is the last release of Kleborate v2, before transitioning to a new modular codebase under v3.0

It includes April 2024 updates to the MLST, virulence and AMR databases, including all updates relevant to the SHV database/logic as described in https://doi.org/10.1101/2024.04.05.587953

What's Changed

• updated allele databases by @Marysteph in #76
• Add setuptools to requirements (Fix #78) by @samuell in #79
• Add --kaptive_path to specify path to kaptive data by @rpetit3 in #59
• adding SHV-238 by @katholt in #81

New Contributors

• @Marysteph made their first contribution in #76
• @samuell made their first contribution in #79
• @rpetit3 made their first contribution in #59

Full Changelog: v2.4.1...v2.5

v2.4.1

This release includes updates to beta-lactamase SHV genotyping (including novel alleles, mutation tracking, and improved assignments to wildtype/ESBL/inhibitor resistant classes), based on the results of the KlebNET AMR Geno-Pheno group.
(It is the same as v2.4.0, but also fixes the SHV unit tests which were not updated for v2.4.0)

v2.4.0

This release includes updates to beta-lactamase SHV genotyping (including novel alleles, mutation tracking, and improved assignments to wildtype/ESBL/inhibitor resistant classes), based on the results of the KlebNET AMR Geno-Pheno group.