Modules for Klebsiella oxytoca species complex#

--preset kosc
Klebsiella species tree

These modules will be run if the enterobacterales__species module confirms the input assembly as a member of the K. oxytoca species complex (KoSC) labelled in the tree above, and listed in the table below.

Klebsiella oxytoca

Klebsiella grimontii

Klebsiella michiganensis

Klebsiella pasteurii

Klebsiella huaxiensis

Klebsiella spallanzanii

MLST#

-m kosc__mlst

Genomes identified as belonging to the K. oxytoca species complex are subjected to MLST using the 7-locus scheme described at the K. oxytoca at PubMLST.

A copy of the MLST alleles and ST definitions is stored in the data/ directory of this module.

Parameters#

--klebsiella_oxytoca_complex__mlst_min_identity

Minimum alignment percent identity for klebsiella_oxytoca_complex MLST (default: 90.0)

--klebsiella_oxytoca_complex__mlst_min_coverage

Minimum alignment percent coverage for klebsiella_oxytoca_complex MLST (default: 80.0)

--klebsiella_oxytoca_complex__mlst_required_exact_matches

At least this many exact matches are required to call an ST (default: 3)

Outputs#

Output of the KoSC MLST module is the following columns:

Column name

Content

ST

sequence type

gapA, infB, mdh, pgi, phoE, rpoB, tonB

allele number

  • Kleborate makes an effort to report the closest matching ST if a precise match is not found.

  • Imprecise allele matches are indicated with a *.

  • Imprecise ST calls are indicated with -nLV, where n indicates the number of loci that disagree with the ST reported. So 258-1LV indicates a single-locus variant (SLV) of ST258, i.e. 6/7 loci match ST258.

Virulence typing#

Genomes identified as belonging to the K. oxytoca species complex are subjected to typing for yersiniabactin, colibactin, aerobactin, salmochelin and rmp loci, using the following modules:

-m klebsiella__ybst, klebsiella__cbst, klebsiella__abst, klebsiella__smst, klebsiella__rmst

These modules were primarily designed for typing of K. pneumoniae species complex, and the databases are populated from variation detected in KpSC genomes (see details on the KpSC modules page here). However they can appear in KoSC genomes and so typing is included in the KoSC preset. A more focused database capturing variation across KoSC is planned.

K and O locus typing#

-m kosc__kaptive

This module will run the Kaptive v3 tool to identify capsule (K) and O antigen loci based on the K. oxytoca species complex database described in this paper. See the Kaptive documentation for more details of how Kaptive works, tutorials, and citations.

Parameters#

-kosc_k

Kaptive database for Kosc K-locus typing

-kosc_o

Kaptive database for Kosc O-locus typing

Outputs#

Kaptive results are output in the following columns: