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.

Kleborate v2.0.3

For this version of Kleborate, we changed the internal logic for how exact amino acid matches are called:

• Previously, we used tblastx to align the assembly's gene sequence to reference alleles, looking for an exact match. However, some cases popped up where this wasn't working due to bizarre BLAST behaviour.
• Now, we use Biopython to translate the assembly's gene sequence and the reference alleles, and then look for a match in the translate sequences. This seems more robust!

Additionally we fixed a bug that occurred in an annoying corner-case:

• Previously, if an allele had a mutated start/stop codon, exact amino acid matches could be missed. This happened because a change at the very start/end of the gene sequence would result in a not-quite-full-length nucleotide match.
• Now, mutated start/stop codons can still give the appropriate exact amino acid match.

Kleborate v2.0.1

Two bug fixes in this release:

• Kleborate now runs Kaptive with the same Python interpreter it's using. Fixes a crash that could happen if you didn't have python3 in your PATH. Thanks, @EricDeveaud!
• The SHV-56 allele was described inconsistently in the FASTA and CSV files, which could cause a crash. Now fixed!