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Legacy Database Information
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.. note::
This page contains information about legacy Kaptive databases for backwards compatibility and interpretation of
old results.
.. _Legacy-Klebsiella-O-locus-database:
Legacy *Klebsiella* O locus database
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The *Klebsiella* O locus database (``Klebsiella_o_locus_primary_reference.gbk``) contains annotated sequences for 13
distinct *Klebsiella* O loci.
O locus classification requires some special logic, as the O1 and O2 serotypes are associated with the same loci and
the distinction between O1 and each of the four defined O2 subtypes (O2a, O2afg, O2ac, O2aeh) is determined by the
presence/absence of 'extra genes' elsewhere in the chromosome as indicated in the table below. Kaptive therefore looks
for these genes to predict antigen (sub)types. (Note that the original implementation of O locus typing in Kaptive
(< v2.0) distinguished O1 and O2 but not the O2 subtypes.)
Read more about the O locus and its classification here: `The diversity of *Klebsiella* pneumoniae surface polysaccharides `_.
Find out about the genetic determinants of O1 and O2 (sub)types here: `Molecular basis for the structural diversity in serogroup O2-antigen polysaccharides in *Klebsiella pneumoniae* `_.
Find out about the O1 glycoforms and their genetic determinants here: `Identification of a second glycoform of the clinically prevalent O1 antigen from *Klebsiella pneumoniae*. `_
Database versions:
* Kaptive v0.4.0 and above include the original version of the *Klebsiella* O locus database, as described in `Wick, R. et al. J Clin Microbiol 2019 `_.
* Kaptive v2.0 and above include a novel O locus reference (O1/O2v3) and updated 'Extra genes' for prediction of O1 and O2 antigen (sub)types, as shown in the table below and described in `Lam, M.M.C et al. 2021. Microbial Genomics 2022. `_
* Kaptive v2.0.8 and above include:
i) updated 'Extra genes' logic for prediction of O1 glycoforms, reported as O1a (isolate predicted to produce O1a
only) and O1ab (isolate predicted to be able to produce both O1a and O1b glycoforms);
ii) OL101 re-assigned as OL13 and its associated phenotype prediction updated to O13, to reflect the
`description of the novel O13 polysaccharide structure `_.
Genetic determinants of O1 and O2 outer LPS antigens as reported in Kaptive:
========= ==================== ================================== ================================= ======================================== ==================================
O locus Extra genes Kaptive < v2.0 (locus\ :sup:`a`) Kaptive v2.0+ (locus\ :sup:`a`) Kaptive v2.0 - v2.0.7 (type\ :sup:`b`) Kaptive v2.0.8+ (type\ :sup:`b`)
========= ==================== ================================== ================================= ======================================== ==================================
O1/O2v1 none O2v1 O1/O2v1 O2a O2a
O1/O2v2 none O2v2 O1/O2v2 O2afg O2afg
O1/O2v3 none Na O1/O2v3 O2a O2a
O1/O2v1 *wbbYZ* O1v1 O1/O2v1 Na O1ab
O1/O2v2 *wbbYZ* O1v2 O1/O2v2 Na O1ab
O1/O2v3 *wbbYZ*. Na O1/O2v3 Na O1ab
O1/O2v1 *wbbY* only O1v1 O1/O2v1 O1 O1a
O1/O2v2 *wbbY* only O1v2 O1/O2v2 O1 O1a
O1/O2v3 *wbbY* only Na O1/O2v3 O1 O1a
O1/O2v1 *wbbY* OR *wbbZ* O1/O2v1 Na Na Na
O1/O2v2 *wbbY* OR *wbbZ* O1/O2v2 Na Na Na
O1/O2v3 *wbbY* OR *wbbZ* Na Na Na Na
O1/O2v1 *wbmVW* Na O1/O2v1 O2ac O2ac
O1/O2v2 *wbmVW* Na O1/O2v2 O2ac O2ac
O1/O2v3 *wbmVW* Na O1/O2v3 O2ac O2ac
O1/O2v1 *gmlABD* Na O1/O2v1 O2aeh O2aeh
O1/O2v2 *gmlABD* Na O1/O2v2 O2aeh O2aeh
O1/O2v3 *gmlABD* Na O1/O2v3 O2aeh O2aeh
O1/O2v1 *wbbY* AND *wbmVW* Na O1/O2v1 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
O1/O2v2 *wbbY* AND *wbmVW* Na O1/O2v2 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
O1/O2v3 *wbbY* AND *wbmVW* Na O1/O2v3 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
========= ==================== ================================== ================================= ======================================== ==================================
- :sup:`a` as reported in the ‘Best match locus’ column in the Kaptive output.
- :sup:`b` predicted antigenic serotype reported in the 'Best match type' column in the Kaptive output (v2.0 and above).
- Na- not applicable