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Full information on isolate 02A029 (id:6)

Projects

This isolate is a member of the following projects:

Public isolates
This project contains the isolates that should be publicly available through the public access database.
published_genomes
All isolates with published genome imported in BIGSdb, and validated for scgMLST_S study
Bialek et al 2014_EID
167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)

Provenance/primary metadata

id
6
isolate
02A029
aliases
02A029; SB14
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
724 updates show details
date entered
2006-09-05
datestamp
2025-05-26
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
1997
city
Brussels
country
Belgium
continent
Europe
source type
Human
host
Human
source details
Blood
source lab
UMCU (Utrecht, NL)
K type
K1

Publications (3)

  • Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
  • Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
  • Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 43:4178-82

Sequence bin

method
Illumina
contigs
84
total length
5,330,811 bp
max length
335,192 bp
mean length
63,463 bp
N50
111,115
L50
15
N90
35,301
L90
45
N95
24,928
L95
53
%GC
57.55
Ns
0
gaps
0
loci tagged
6,908

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_S62962699
Kpn_cgMLST2752270198

Analysis

rMLST species identification

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

Analysis performed: 2025-01-28

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 99.99% 100.00% 0 bp 20 / 20 (100.00%) 0 0 / 20 (0.00%) 4 KL40_03_wcpO,97.97%,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 ?2 99.32% 100.03% n/a 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,98.56%,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

2025-12-28T18:55:29.428467 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T18:55:33.624068 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
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
68
Colibactin
clb 2
clbA
2
clbB
2
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
2
clbI
2
clbL
2
clbM
2
clbN
2
clbO
2
clbP
2
clbQ
2
AbST
0
SmST
0
RmST
0
virulence_score
2
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
99.99%
O_locus
OL2α.2
O_type
O1αβ,2β
O_locus_confidence
Typeable
O_locus_problems
?2
O_locus_identity
99.32%

Analysis performed: 2026-01-15; Kleborate v3.2.4

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_429_0_42_0_1_0_0_0
Phylogroup
Kp1
Sublineage
SL23
Clonal group
CG23

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_42_076
0_0_429_0_42_0_144
0_0_429_0_42_0_1_022
0_0_429_0_42_0_1_0_012
0_0_429_0_42_0_1_0_0_002
061041312
0_058541312
0_0_429190492
0_0_429_043490
0_0_429_0_421013
0_0_429_0_42_076
0_0_429_0_42_0_144
0_0_429_0_42_0_1_022
0_0_429_0_42_0_1_0_012
0_0_429_0_42_0_1_0_0_002

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

Tools

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