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Full information on isolate IPEUC-1570 (id:375)

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
375
isolate
IPEUC-1570
aliases
IPEUC-1570; SB3310
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history
737 updates show details
date entered
2009-02-10
datestamp
2025-07-18
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
1988
city
Paris
country
France
continent
Europe
source type
Animal
host
Horse
source details
Unknown
infection
Metritis
other source info
Mare
source lab
Institut Pasteur
K type
K1

Publications (2)

  • 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

Sequence bin

method
Illumina
contigs
106
total length
5,583,646 bp
max length
440,598 bp
mean length
52,676 bp
N50
114,796
L50
13
N90
35,845
L90
45
N95
19,959
L95
55
%GC
57.20
Ns
0
gaps
0
loci tagged
4,254

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 99.93% 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

2025-12-28T18:56:50.885800 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T18:56:55.153731 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
341
Yersiniabactin
ybt 1; ICEKp10
ybtS
2
ybtX
2
ybtQ
2
ybtP
2
ybtA
2
irp2
6
irp1
12
ybtU
2
ybtT
2
ybtE
2
fyuA
2
CbST
13-2LV
Colibactin
clb 3
clbA
2
clbB
3
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
4
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
2
rmpC
17
virulence_score
5
AGly_acquired
aph3-Ia.v1^
Bla_chr
SHV-11^
SHV_mutations
SHV:p.Leu35Gln
spurious_resistance_hits
ant(3'')-IIa*?-11%
resistance_score
0
num_resistance_classes
1
num_resistance_genes
1
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
99.93%
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_44_1_1_0_1_0
Phylogroup
Kp1
Sublineage
SL23
Clonal group
CG23

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_44_1719
0_0_429_0_44_1_1411
0_0_429_0_44_1_1_029
0_0_429_0_44_1_1_0_114
0_0_429_0_44_1_1_0_1_004
061041312
0_058541312
0_0_429190492
0_0_429_043490
0_0_429_0_441049
0_0_429_0_44_1719
0_0_429_0_44_1_1411
0_0_429_0_44_1_1_029
0_0_429_0_44_1_1_0_114
0_0_429_0_44_1_1_0_1_004

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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