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Full information on isolate SA2 (id:1516)

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
1516
isolate
SA2
aliases
SA2; SB4384
sender
Suzanne Bialek, AP-HP
curator
Auto Tagger
update history
719 updates show details
date entered
2013-03-29
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
city
Paris
country
France
continent
Europe
source type
Human
host
Human
source details
Blood
infection
Liver abscess
K type
K1
K typing method
PCR

Publication (1)

  • 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

Sequence bin

method
Illumina
contigs
223
total length
5,719,746 bp
max length
173,207 bp
mean length
25,650 bp
N50
50,483
L50
30
N90
16,391
L90
103
N95
9,414
L95
125
%GC
56.92
Ns
0
gaps
0
loci tagged
4,079

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_S62962899

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,97.97%,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 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,98.56%,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

2025-12-28T18:58:00.887130 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T18:58:05.933862 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
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
26-1LV
RmpADC
rmp 1; KpVP-1
rmpA
2
rmpD
29
rmpC
2
virulence_score
5
rmpA2
rmpA2_3-47%
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_58_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL23
Clonal group
CG23

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_58_071
0_0_429_0_58_0_041
0_0_429_0_58_0_0_021
0_0_429_0_58_0_0_0_011
0_0_429_0_58_0_0_0_0_001
061041312
0_058541312
0_0_429190492
0_0_429_043490
0_0_429_0_58101
0_0_429_0_58_071
0_0_429_0_58_0_041
0_0_429_0_58_0_0_021
0_0_429_0_58_0_0_0_011
0_0_429_0_58_0_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

Tools

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