Skip to content

Commit 717746b

Browse files
kelwyreskelwyres
authored
Merge pull request #41 from tomdstanton/Update-O-Nomenclature
Update version to v3.1.0 Updating KpSC O-locus nomenclature as described in: Whitfield et al. O-antigen polysaccharides in Klebsiella pneumoniae: structures and molecular basis for antigenic diversity. Microbiology and Molecular Biology Reviews 21:e0009023. DOI: 10.1128/mmbr.00090-23
2 parents 9a3604a + 0e821d6 commit 717746b

File tree

12 files changed

+4317
-4715
lines changed

12 files changed

+4317
-4715
lines changed

‎README.md‎

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,17 @@
11
<p align="center"><img src="extras/kaptive_logo.png" alt="Kaptive" width="400"></p>
22

3+
[![DOI:10.1101/22025.02.05.636613](http://img.shields.io/badge/DOI-10.1101/2025.02.05.636613-B31B1B.svg)](https://doi.org/10.1101/2025.02.05.636613)
4+
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14000416.svg)](https://doi.org/10.5281/zenodo.14000416)
5+
36

47
Kaptive reports information about surface polysaccharide loci for _Klebsiella pneumoniae_ species complex and _Acinetobacter baumannii_ genome assemblies. You can also run a graphical version of Kaptive via [this web interface](http://kaptive-web.erc.monash.edu/) ([source code](https://github.com/kelwyres/Kaptive-Web)).
58

69
**For information on how to install, run, interpret and cite Kaptive please visit the [Docs](https://kaptive.readthedocs.io/en/latest/).**
710

811
A step-by-step tutorial for the most recent version is available [here](https://docs.google.com/document/d/1EXZanC6uCbhAniVyJn91HOVD8JF6DLRZxmFPGs_nlME/edit?usp=sharing) (Kaptive v3). The tutorial for the previous version is [here](https://bit.ly/kaptive-workshop).
912

10-
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11257262.svg)](https://doi.org/10.5281/zenodo.11257262)
13+
If you use Kaptive in your research, please cite:
14+
15+
Stanton TD, Hetland MAK, Löhr IH, Holt KE, Wyres KL. Fast and Accurate in silico Antigen Typing with Kaptive 3
16+
[Internet]. bioRxiv; 2025 [cited 2025 Feb 27]. p. 2025.02.05.636613.
17+
Available from: https://www.biorxiv.org/content/10.1101/2025.02.05.636613v1

‎docs/source/Databases.rst‎

Lines changed: 45 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -125,16 +125,14 @@ KL22, the phenotype is predicted as 'K37', the non-acetylated version of the K22
125125

126126
Let's look at an example that uses extra genes outside of the locus (from the *K. pneumoniae* O locus database):
127127

128-
======================= ============ ===================
129-
loci genes phenotype
130-
======================= ============ ===================
131-
O1/O2v1;O1/O2v2;O1/O2v3 wbbY O1a
132-
O1/O2v1;O1/O2v2;O1/O2v3 wbbY;wbbZ O1ab
133-
======================= ============ ===================
128+
======================= ================ ==========
129+
loci genes phenotype
130+
======================= ================ ==========
131+
OL2α.1;OL2α.2;OL2α.3 orf8 O2αγ
132+
======================= ================ ==========
134133

135-
Here, the first line states that if *wbbY* is present in a genome carrying any of the O1/O2v1, O1/O2v2, or O1/O2v3 loci, the phenotype
136-
will be predicted as 'O1a'. The second line states that if **both** *wbbY* and *wbbZ* are present in a genome carrying any of the
137-
same loci, the phenotype will instead be predicted as 'O1ab'.
134+
Here, the first line states that if *orf8* is present in a genome carrying any of the OL2α.1, OL2α.2 or OL2α.3 loci,
135+
the phenotype will be predicted as 'O2αγ'.
138136

139137
.. note::
140138
Each specific locus and gene is delimited by a semicolon.
@@ -227,65 +225,48 @@ KL37 Removed from the database
227225
*Klebsiella* O locus database
228226
------------------------------
229227

228+
In Kaptive 3.1.0, we introduced new O-antigen nomenclature in the *Klebsiella* O locus database
229+
(``Klebsiella_o_locus_primary_reference.gbk``) along wth the publication of this review:
230+
`O-antigen polysaccharides in Klebsiella pneumoniae: structures and molecular basis for antigenic diversity <https://journals.asm.org/doi/full/10.1128/mmbr.00090-23#T1>`_.
231+
230232
The *Klebsiella* O locus database (``Klebsiella_o_locus_primary_reference.gbk``) contains annotated sequences for 13
231233
distinct *Klebsiella* O loci.
232234

233235
O locus classification requires some special logic, as the O1 and O2 serotypes are associated with the same loci and
234-
the distinction between O1 and each of the four defined O2 subtypes (O2a, O2afg, O2ac, O2aeh) is determined by the
235-
presence/absence of 'extra genes' elsewhere in the chromosome as indicated in the table below. Kaptive therefore looks
236-
for these genes to predict antigen (sub)types. (Note that the original implementation of O locus typing in Kaptive
237-
(< v2.0) distinguished O1 and O2 but not the O2 subtypes.)
238-
239-
Read more about the O locus and its classification here: `The diversity of *Klebsiella* pneumoniae surface polysaccharides <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320592/>`_.
240-
241-
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* <https://pubmed.ncbi.nlm.nih.gov/29602878/>`_.
236+
the distinction between O1 and each of the defined O2 subtypes (2α, 2β, 2γ) is determined by the
237+
presence/absence of 'extra genes' (gml2β and orf8) elsewhere in the chromosome as indicated in the table below.
238+
Kaptive therefore looks for these genes to predict antigen (sub)types.
242239

243-
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*. <https://doi.org/10.1073/pnas.2301302120>`_
244-
245-
Database versions:
240+
.. note::
241+
You can find information about the *Klebsiella* O locus database in Kaptive versions <3.1.0 :ref:`here <Legacy-Klebsiella-O-locus-database>`.
242+
243+
========================== ===================================================== =============================================== ==============================================
244+
New serotype designation Required genes/loci (implemented in Kaptive v.3.1+) Prior Kaptive designation (v.2.0.8–v.3.0.0b6) Prior Kaptive genes/loci (v.2.0.8–v.3.0.0b6)
245+
========================== ===================================================== =============================================== ==============================================
246+
O1αβ,2α OL2α.(1/2/3), wbbYZ O1ab O1/O2v1, wbbYZ
247+
O1α,2α OL2α.(1/2/3), wbbY O1a O1/O2v1, wbbY
248+
O1αβ,2β OL2α.(1/2/3), gml2β, wbbYZ O1ab O1/O2v2, wbbYZ
249+
O1α,2β OL2α.(1/2/3), gml2β, wbbY O1a O1/O2v2, wbbY
250+
O1αβ,2γ OL2α.(1/2/3), orf8, wbbYZ O1ab O1/O2v3, wbbYZ
251+
O2α OL2α.(1/2/3) O2a O1/O2v1
252+
O2β OL2α.(1/2/3), gml2β O2afg O1/O2v2
253+
O2αγ OL2α.(1/2/3), orf8 O2a O1/O2v3
254+
O3α + O3β OL3α/β O3/O3a O3/O3a
255+
O3γ OL3γ O3b O3b
256+
O4 OL4 O4 O4
257+
O5 OL5 O5 O5
258+
O10 OL10 OL103 OL103
259+
O11αβ,2α OL2α.(1/2/3), wbmVWX O2ac O1/O2v1, wbmVWX
260+
O11α,2α OL2α.(1/2/3), wbmVW O2ac O1/O2v1, wbmVW
261+
O11αβ,2β OL2α.(1/2/3), gml2β, wbmVWX O2ac O1/O2v2, wbmVWX
262+
O11α,2β OL2α.(1/2/3), gml2β, wbmVW O2ac O1/O2v2, wbmVW
263+
O11αβ,2γ OL2α.(1/2/3), orf8, wbmVWX O2ac O1/O2v3, wbmVW
264+
O12 OL12 O12 O12
265+
O13 OL13 O13 OL13
266+
O14 OL14 OL102 OL102
267+
O15 OL15 OL104 OL104
268+
========================== ===================================================== =============================================== ==============================================
246269

247-
* 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 <http://jcm.asm.org/content/56/6/e00197-18>`_.
248-
* 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. <https://doi.org/10.1099/mgen.0.000800>`_
249-
* Kaptive v2.0.8 and above include:
250-
251-
i) updated 'Extra genes' logic for prediction of O1 glycoforms, reported as O1a (isolate predicted to produce O1a
252-
only) and O1ab (isolate predicted to be able to produce both O1a and O1b glycoforms);
253-
254-
ii) OL101 re-assigned as OL13 and its associated phenotype prediction updated to O13, to reflect the
255-
`description of the novel O13 polysaccharide structure <https://www.sciencedirect.com/science/article/pii/S0144861723010469>`_.
256-
257-
Genetic determinants of O1 and O2 outer LPS antigens as reported in Kaptive:
258-
259-
========= ==================== ================================== ================================= ======================================== ================================== ==
260-
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`)
261-
========= ==================== ================================== ================================= ======================================== ================================== ==
262-
O1/O2v1 none O2v1 O1/O2v1 O2a O2a
263-
O1/O2v2 none O2v2 O1/O2v2 O2afg O2afg
264-
O1/O2v3 none Na O1/O2v3 O2a O2a
265-
O1/O2v1 *wbbYZ* O1v1 O1/O2v1 Na O1ab
266-
O1/O2v2 *wbbYZ* O1v2 O1/O2v2 Na O1ab
267-
O1/O2v3 *wbbYZ*. Na O1/O2v3 Na O1ab
268-
O1/O2v1 *wbbY* only O1v1 O1/O2v1 O1 O1a
269-
O1/O2v2 *wbbY* only O1v2 O1/O2v2 O1 O1a
270-
O1/O2v3 *wbbY* only Na. O1/O2v3 O1 O1a
271-
O1/O2v1 *wbbY* OR *wbbZ* O1/O2v1 Na Na Na
272-
O1/O2v2 *wbbY* OR *wbbZ* O1/O2v2 Na Na Na
273-
O1/O2v3 *wbbY* OR *wbbZ* Na Na Na Na
274-
O1/O2v1 *wbmVW* Na O1/O2v1 O2ac O2ac
275-
O1/O2v2 *wbmVW* Na O1/O2v2 O2ac O2ac
276-
O1/O2v3 *wbmVW* Na O1/O2v3 O2ac O2ac
277-
O1/O2v1 *gmlABD* Na O1/O2v1 O2aeh O2aeh
278-
O1/O2v2 *gmlABD* Na O1/O2v2 O2aeh O2aeh
279-
O1/O2v3 *gmlABD* Na O1/O2v3 O2aeh O2aeh
280-
O1/O2v1 *wbbY* AND *wbmVW* Na O1/O2v1 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
281-
O1/O2v2 *wbbY* AND *wbmVW* Na O1/O2v2 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
282-
O1/O2v3 *wbbY* AND *wbmVW* Na O1/O2v3 O1 (O2ac)\ :sup:`b` O1 (O2ac)\ :sup:`b`
283-
========= ==================== ================================== ================================= ======================================== ================================== ==
284-
285-
286-
- :sup:`a` as reported in the ‘Best match locus’ column in the Kaptive output.
287-
- :sup:`b` predicted antigenic serotype reported in the 'Best match type' column in the Kaptive output (v2.0 and above).
288-
- Na- not applicable
289270

290271
*Acinetobacter baunannii* K and OC locus databases
291272
----------------------------------------------------
@@ -412,6 +393,6 @@ Which would create two files: ``KL1.faa`` and ``KL2.faa``.
412393
kaptive assembly kpsc_k assembly.fasta -j kaptive_results.json
413394

414395
.. warning::
415-
It is possible to write **all** text formats (FNA, FAA and FFN) to the same file (including stdout), however
416-
this is not recommended for downstream analysis.
396+
It is possible to write **all** text formats (``fna``, ``faa`` and ``ffn``) to the same file (including stdout),
397+
however this is not recommended for downstream analysis.
417398

0 commit comments

Comments
 (0)