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.

Kleborate v2.3.2

This release fixes the version mismatch between the release and running kleborate --version (see #68, thanks @kapsakcj and @singuyenmai), but is otherwise identical to the previous release.

Kleborate v2.3.1

This release fixes some failing unit tests (see #67, thanks @kapsakcj), but is otherwise identical to v2.3.0.

Kleborate v2.3.0

Changes since v2.2.0 include:

• Updated virulence alleles/profiles
• Change in sequence of iucA alleles with length ~1791bp to ~1725bp; see note in Wiki (Typing available in Kleborate > Acquired Virulence loci > Aerobactin and Salmochelin) for more details
• Retirement of iucA_48, iucA_49 and iucA_52
• Retirement of AbST 70, 82, 83

Bug fixes:

• Amended the mismatched antibiotic class for 3 entries in CARD_v3.1.13.fasta file to match CARD_AMR_clustered.csv, which can cause a crash; tet(X1), tet(X5), tet(X6) incorrectly assigned as 'Tet', amended to 'Tgc'. Thanks @learithe and @nquynh8991

Kleborate v2.2.0

Changes since v2.1.0:

• Additional AMR genes added to database.
• Updated Kaptive to v2, which makes the distinction between loci and types and includes better logic for O subtypes.

Kleborate v2.1.0

Changes since v2.0.4 include:

• Updated chromosomal MLST alleles/profiles
• Updated virulence MLST alleles/profiles
• Updated species classification database
• When a virulence locus contains any truncated genes, (truncated) will be appended to the lineage/element

Kleborate v2.0.4

Two changes in this version:

• There is now a minimum threshold for Kaptive confidence, below which loci will be reported as 'unknown'.

  • For example, if Kaptive found a best K locus of KL102 but with a confidence of None, it will now be reported as unknown (best match = KL102) in Kleborate.
  • The default minimum confidence level is 'Good' and this can be changed with Kleborate's new --min_kaptive_confidence setting.

• We made some cosmetic changes to the help text, including the display of default values for settings.