This repository houses databases for in silico typing of K. pneumoniae Species Complex (KpSC) K and O surface polysaccharides using Kaptive. The capsule polysaccharide (K) and outer-lipopolysaccharide (O) are major surface antigens and phage binding receptors, making them key targets for novel vaccines, monoclonal antibody and phage therapies targeting KpSC.
Genomic typing approaches have helped reveal extensive K and O polysaccharide variation among natural KpSC populations, and power large scale seroepidemiology analyses. To learn more about genomic analyses and seroepidemiology of KpSC, check out the training materials here.
Warning
These databases should not be used for species outside of the KpSC! Using the databases to type other organisms, including other Klebsiella species, may result in errors and low typing rates.
Tip
K and O locus databases for the Klebsiella oxytoca Species Complex are available here.
- What is the K. pneumoniae Species Complex?
- Database formats and versions
- Citations
- Curators
- Contribute
- License
The K. pneumoniae Species Complex (KpSC) comprises K. pneumoniae and closely related organisms that cannot be accurately distinguished by standard biochemical or mass-spectometry-based identification protocols (see table and phylogeny below). We've included the phylogroup numbers in the table below for backwards compatibility with older literature, but these names are no longer recommended for use. See this review for an overview of the species complex.
| Species | Kp phylogroupa | Kp phylogroup (alternative)b | Reference |
|---|---|---|---|
| K. pneumoniae | Kp1 | KpI | Brenner, D.J. 1979 Int J Syst Evol Microbiol 29: 38-41 |
| K. quasipneumoniae subsp quasipneumoniae | Kp2 | KpIIa | Brisse et al., 2014 Int J Syst Evol Microbiol 64:3146-52 |
| K. quasipneumoniae subsp similipneumoniae | Kp4 | KpIIb | Brisse et al. 2014 Int J Syst Evol Microbiol 64:3146-52 |
| K. variicola subsp variicola | Kp3 | KpIII | Rosenblueth et al. 2004 Syst Appl Microbiol 27:27-35 |
| K. variicola subsp tropica | Kp5 | - | Rodrigues et al., 2019 Res Microbiol S0923-2508:30019-1 (described as subsp tropicalensis in paper) |
| K. quasivariicola | Kp6 | - | Long et al. 2017 Genome Announc 5: e01057-17 |
| K. africana | Kp7 | - | Rodrigues et al. 2019 Res Microbiol S0923-2508:30019-1 (described as africanensis in this paper) |
a Kp phylogroup numbers as described in Rodrigues et al. 2019
b alternative (older) Kp phylogroup numbers as described in Brisse et al. 2001 and Fevre et al. 2005 prior to the identification of K. variicola subsp tropica, K. quasivariicola and K. africana.
The K and O locus databases each comprise two files that are required to run Kaptive:
- A multi-genbank file containing each unique locus sequence and its gene annotations.
- A metadata file in TOML format, which provides essential information about the database (e.g. version, target organism(s), curator details), plus any special phenotype logic that applies to the database.
Please see the Kaptive docs for more details on the database file formats.
Loci are defined by the rules of the Kaptive typing framework, which states that a unique locus should represent a unique set of genes, with the assumption that this encodes a unique polysaccharide structure. In many cases, these unique structures will result in unique immunological serotypes.
The gene translations (protein sequences) from each locus are compared by pairwise alignment, and must fall under a defined percent identity threshold to be considered 'unique'. Some genes (such as the core assembly machinery) will be highly similar, however the genes responsible for the polysaccharide structural diversity are expected to be more variable. The gene identity threshold for the KpSC databases is 82.5%.
In some cases, specific nucleotide variations within loci and/or additional genes located elsewhere in the genome are known to result in modifications to the resulting polysaccharide structure. Where the impact of these variations or additional genes is well understood, they are captured within the databases using the phenotype logic section of the metadata file and the 'extra genes' entries within the multi-genbank file (see below for examples).
The KpSC K locus reference database
(Klebsiella_pneumoniae_Species_Complex_K) comprises full-length
(galF to ugd) annotated sequences for each distinct KpSC K
locus, where available:
- K loci KL1-KL72, KL74 and KL79-KL82 correspond to the originally defined K-types K1-K72, K74 and K79-K82, respectively.
- KL101 and above were defined from DNA sequence data on the basis of gene content, numbered by order of discovery. At the time of discovery, no matched phenotypes were known; however, the polysaccharide structures and/or serotypes corresponding to several of these loci have since been described e.g. serotypes K102, K112, K122, K136 and K149).
Note
Insertion sequences (IS) are excluded from this database since we assume that the ancestral sequence was likely IS-free and IS transposase genes are not specific to the K locus. Synthetic IS-free K locus sequences were generated for K loci for which no naturally occurring IS-free variants have been identified to date.
- v0.5.1 and below (previously distributed with Kaptive) include the original KpSC K locus databases, as described in Wyres, K. et al. Microbial Genomics 2016.
- v0.6.0 and above (previously distributed with Kaptive) include four novel KpSC K locus references (KL162-KL165), described in Wyres et al. Genome Medicine 2020.
- v0.7.1 and above (previously distributed with Kaptive) contain updated versions of the KL53 and KL126 loci (see table below for details). The updated KL126 locus sequence is described in McDougall, F. et al. Research in Microbiology 2021.
- v0.7.2 and above (previously distributed with Kaptive) include a novel K locus reference (KL166), described in Le, MN. et al. Microbial Genomics 2022.
- v0.7.3 and above (previously distributed with Kaptive) include four novel K locus references (KL167-KL170), described in Gorrie, C. et al. Nature Communications 2022.
- v2.0.0 and above (previously distributed with Kaptive) include 16 novel K locus references (KL171-KL186) and described in Lam, M.M.C et al. Microbial Genomics 2022.
- v3.0.0 and above (previously distributed with Kaptive), the original KL37 locus was removed since under the Kaptive typing framework, this locus is identical to KL22 (i.e. they contain the same set of genes), differing only by a frameshift mutation in an aceytyltransferase gene which results in the loss of an acetyl group from the K37 polysaccharide structure. From v3.0 onwards we include an explicit prediction of the K37 phenotype based on the presence of the KL22 locus with truncated acetyltransferase. Kaptive will report these genomes as
Best match locus: KL22,Best match type: K37. - v3.2.0 and above (previously distributed with Kaptive) introduced a re-annotation of the K locus reference genes curated by Dr. Tom Stanton and A/Prof Johanna Kenyon. All K-locus genes where thoroughly screened against curated annotations with a variety of homology detection methods to provide a more accurate functional description and standardised gene nomenclature.
| Locus | Change | Reason | Date of change | Version |
|---|---|---|---|---|
| KL53 | Annotation update: wcaJ changed to wbaP | Error in original annotation | 21 July 2020 | v 0.7.1 |
| KL126 | Sequence update: new sequence from isolate FF923 includes rmlBADC genes between gnd and ugd | Assembly scaffolding error in original sequence from isolate A-003-I-a-1 | 21 July 2020 | v 0.7.1 |
| KL37 | Removed from the database | Locus is a deletion (atr) variant of KL22 | 22 March 2024 | v 3.0.0 |
| All | Updated gene names and functional annotations | Database standardisation | March 2026 | v 3.2.0 |
From v3.1.0, we introduced new O-antigen nomenclature in the
KpSC O locus database
(Klebsiella_pneumoniae_SC_O.gbk) along wth the publication
of this review: O-antigen polysaccharides in Klebsiella pneumoniae:
structures and molecular basis for antigenic
diversity.
We have also summarised the O-antigen nomenclature update on the Wyres Lab website.
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 defined O2 subtypes (2α, 2β, 2γ) is determined by the presence/absence of 'extra genes' (gml2β and orf8) elsewhere in the chromosome as indicated in the table below. Kaptive therefore looks for these genes to predict antigen (sub)types.
Note
You can find information about the O locus database in versions <3.1.0 here.
| New serotype designation | Required genes/loci (implemented in v.3.1+) | Prior designation (v.2.0.8–v.3.0.0b6) | Prior genes/loci (v.2.0.8–v.3.0.0b6) |
|---|---|---|---|
| O1αβ,2α | OL2α.(1/2/3), wbbYZ | O1ab | O1/O2v1, wbbYZ |
| O1α,2α | OL2α.(1/2/3), wbbY | O1a | O1/O2v1, wbbY |
| O1αβ,2β | OL2α.(1/2/3), gml2β, wbbYZ | O1ab | O1/O2v2, wbbYZ |
| O1α,2β | OL2α.(1/2/3), gml2β, wbbY | O1a | O1/O2v2, wbbY |
| O1αβ,2γ | OL2α.(1/2/3), orf8, wbbYZ | O1ab | O1/O2v3, wbbYZ |
| O2α | OL2α.(1/2/3) | O2a | O1/O2v1 |
| O2β | OL2α.(1/2/3), gml2β | O2afg | O1/O2v2 |
| O2αγ | OL2α.(1/2/3), orf8 | O2a | O1/O2v3 |
| O3α + O3β | OL3α/β | O3/O3a | O3/O3a |
| O3γ | OL3γ | O3b | O3b |
| O4 | OL4 | O4 | O4 |
| O5 | OL5 | O5 | O5 |
| O10 | OL10 | OL103 | OL103 |
| O11αβ,2α | OL2α.(1/2/3), wbmVWX | O2ac | O1/O2v1, wbmVWX |
| O11α,2α | OL2α.(1/2/3), wbmVW | O2ac | O1/O2v1, wbmVW |
| O11αβ,2β | OL2α.(1/2/3), gml2β, wbmVWX | O2ac | O1/O2v2, wbmVWX |
| O11α,2β | OL2α.(1/2/3), gml2β, wbmVW | O2ac | O1/O2v2, wbmVW |
| O11αβ,2γ | OL2α.(1/2/3), orf8, wbmVWX | O2ac | O1/O2v3, wbmVW |
| O12 | OL12 | O12 | O12 |
| O13 | OL13 | O13 | OL13 |
| O14 | OL14 | OL102 | OL102 |
| O15 | OL15 | OL104 | OL104 |
If you use the K locus database please cite:
Wyres et al. 2016. Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics:2(12) DOI: https://doi.org/10.1099/mgen.0.000102.
If you use the O locus database please cite:
Wick et al. 2018. Kaptive Web: User-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes. Journal of Clinical Microbiology:56(6) DOI: https://doi.org/10.1128/jcm.00197-18
These databases were originally developed by Kelly Wyres, Kathryn Holt and Ryan Wick, and are now maintained by Kelly Wyres, Tom Stanton and Naoise McGarry (Monash University, Australia).
If you think you've found a novel K or O locus please get in touch so we can add it to the database (with attribution)!
The databases are distributed under GNU Genral Public license v3.0.