Legacy Database Information¶
Note
This page contains information about legacy Kaptive databases for backwards compatibility and interpretation of old results.
Legacy Klebsiella pneumoniae Species Complex O locus database¶
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: 1) 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); 2) 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 (locusa) | Kaptive v2.0+ (locusa) | Kaptive v2.0 - v2.0.7 (typeb) | Kaptive v2.0.8+ (typeb) |
|---|---|---|---|---|---|
| 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)b | O1 (O2ac)b |
| O1/O2v2 | wbbY AND wbmVW | Na | O1/O2v2 | O1 (O2ac)b | O1 (O2ac)b |
| O1/O2v3 | wbbY AND wbmVW | Na | O1/O2v3 | O1 (O2ac)b | O1 (O2ac)b |
- a as reported in the ‘Best match locus’ column in the Kaptive output.
- b predicted antigenic serotype reported in the 'Best match type' column in the Kaptive output (v2.0 and above).
- Na- not applicable