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Full information on isolate SAKP02 (id:9642)

Projects

This isolate is a member of the following project:

Rollin et al 2022_IJID
Collection of K. pneumoniae genomes studied in "Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities" (PMID: 34767984)

Provenance/primary metadata

id
9642
isolate
SAKP02
alias
SA77
sender
Guillaume Rollin, Beaujon hospital, Paris, France
curator
Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history
11 updates show details
date entered
2019-09-03
datestamp
2026-02-12
taxonomic designation
K. pneumoniae
QC status
0000
isolation year
2013
city
Colombes
country
France
continent
Europe
host
Human
source details
CSF
infection
Meningitis
K type
K1

Publication (1)

  • Rollin G, Rossi B, Brisse S, Decré D, Leflon-Guibout V, Bert F, Hoffmann I, Decousser JW, Fantin B, Lefort A (2022). Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities. Int J Infect Dis 114:185-191

Sequence bin

method
Illumina
contigs
107
total length
5,614,398 bp
max length
765,708 bp
mean length
52,472 bp
N50
314,607
L50
5
N90
72,748
L90
19
N95
50,762
L95
23
%GC
57.22
Ns
0
gaps
0
loci tagged
786

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962799

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella pneumoniae Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae 100%

Analysis performed: 2022-11-02

Kaptive

Database Best match locusBest match typeMatch confidenceProblemsIdentityCoverageLength discrepancyExpected genes in locusMissing expected genesOther genes in locusOther genes in locus, detailsExpected genes outside locusExpected genes outside locus, detailsOther genes outside locusOther genes outside locus, detailsTruncated genes, detailsExtra genes, details
Klebsiella K locus KL1 K1 Typeable 99.98% 100.00% 0 bp 20 / 20 (100.00%) 0 0 / 20 (0.00%) 4 KL40_03_wcpO,97.77%,100.00%;KL40_04,99.50%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00%
Klebsiella O locus OL2α.2 O1αβ,2β Typeable 99.29% 100.00% -2 bp 7 / 7 (100.00%) 0 0 / 7 (0.00%) 2 OL3γ_01_manC,99.58%,100.00%;OL3α/β_02_manB,99.78%,97.39% Extra_genes_wbbYZ_02_wbbY,100.00%,100.00%;Extra_genes_gml2β_03_gmlC,98.35%,100.00%;Extra_genes_gml2β_02_gmlB,99.69%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00%

Klebsiella K locus

2025-12-28T19:04:44.675062 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T19:04:48.908631 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Analysis performed: 2025-12-28; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.

Kleborate

species
Klebsiella pneumoniae
species_match
strong
YbST
47-1LV
Yersiniabactin
ybt 1; ICEKp10
ybtS
2
ybtX
2
ybtQ
2
ybtP
2
ybtA
2
irp2
6*
irp1
6
ybtU
2
ybtT
2
ybtE
2
fyuA
2
CbST
29
Colibactin
clb 2
clbA
2
clbB
2
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
3
clbI
2
clbL
2
clbM
2
clbN
2
clbO
2
clbP
2
clbQ
2
AbST
1
Aerobactin
iuc 1
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
SmST
2
Salmochelin
iro 1
iroB
1
iroC
4
iroD
1
iroN
1
RmST
26
RmpADC
rmp 1; KpVP-1
rmpA
2
rmpD
2
rmpC
2
virulence_score
5
Bla_chr
SHV-11^
SHV_mutations
SHV:p.Leu35Gln
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Ciprofloxacin_prediction
wildtype S
Ciprofloxacin_profile_support
90.99% S (N=5168/5680)
Ciprofloxacin_profile
0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
Ciprofloxacin_MIC_prediction
0.25 mg/L [0.25-0.25]
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_confidence
Typeable
K_locus_identity
99.98%
O_locus
OL2α.2
O_type
O1αβ,2β
O_locus_confidence
Typeable
O_locus_identity
99.29%

Analysis performed: 2025-12-28; Kleborate v3.2.4

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_429_0_42_4_0_0_0_0
Phylogroup
Kp1
Sublineage
SL23
Clonal group
CG23

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_42_471
0_0_429_0_42_4_041
0_0_429_0_42_4_0_021
0_0_429_0_42_4_0_0_011
0_0_429_0_42_4_0_0_0_001
061041312
0_058541312
0_0_429190492
0_0_429_043490
0_0_429_0_421013
0_0_429_0_42_471
0_0_429_0_42_4_041
0_0_429_0_42_4_0_021
0_0_429_0_42_4_0_0_011
0_0_429_0_42_4_0_0_0_001

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (185 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (185 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (185 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (185 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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