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Full information on isolate cur15505 (id:62)

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
62
isolate
cur15505
alias
SB2390
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history
721 updates show details
date entered
2006-09-05
datestamp
2025-07-18
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2002
city
Curacao
country
Curacao
continent
South America
source type
Human
host
Human
source details
Urinary tract
source lab
UMCU (Curacao)
K type
K2
K typing method
C-pattern

Publications (5)

  • 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
  • Blin C, Passet V, Touchon M, Rocha EPC, Brisse S (2017). Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 19:1881-1898
  • 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
  • van Westreenen M, Paauw A, Fluit AC, Brisse S, van Dijk W, Verhoef J (2003). Occurrence and spread of SHV extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates in Curacao. J Antimicrob Chemother 52:530-2

Sequence bin

method
Illumina
contigs
11
total length
5,658,175 bp
max length
3,152,981 bp
mean length
514,380 bp
N50
3,152,981
L50
1
N90
350,236
L90
5
N95
110,871
L95
7
%GC
57.10
Ns
34919
gaps
64
loci tagged
4,175

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_S629629100

Analysis

rMLST species identification

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

Analysis performed: 2022-11-02

Kleborate

species
Klebsiella pneumoniae
species_match
strong
QC_warnings
ambiguous_bases
YbST
106
Yersiniabactin
ybt 10; ICEKp4
ybtS
3
ybtX
3
ybtQ
4
ybtP
3
ybtA
3
irp2
7
irp1
7
ybtU
3
ybtT
3
ybtE
3
fyuA
3
CbST
0
AbST
0
SmST
0
RmST
0
virulence_score
1
AGly_acquired
strB.v1;strA.v1;aadA1.v1;aadA2^;aac(6')-Il
MLS_acquired
Mrx;mphA
Tmt_acquired
dfrA12
truncated_resistance_hits
sul1-0%
resistance_score
0
num_resistance_classes
3
num_resistance_genes
8
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
wzi2
K_locus
KL2
K_type
K2
K_locus_confidence
Typeable
K_locus_identity
99.83%
O_locus
OL2α.1
O_type
O1αβ,2α
O_locus_confidence
Typeable
O_locus_identity
100.00%

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

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_1_1_0_1_1_0_0_0
Phylogroup
Kp1
Sublineage
SL14
Clonal group
CG14

Show all thresholds

PrefixThresholdMatching isolates
0_0_1_1_0_1779
0_0_1_1_0_1_1452
0_0_1_1_0_1_1_0216
0_0_1_1_0_1_1_0_0111
0_0_1_1_0_1_1_0_0_006
061041312
0_058541312
0_0_11901229
0_0_1_1431093
0_0_1_1_01095
0_0_1_1_0_1779
0_0_1_1_0_1_1452
0_0_1_1_0_1_1_0216
0_0_1_1_0_1_1_0_0111
0_0_1_1_0_1_1_0_0_006

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-linkage190experimental1 (867 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental81 (177 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental502 (35 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental562 (26 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental665 (12 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental812 (12 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental938 (10 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental1112 (6 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental1 (867 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental81 (177 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental502 (35 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental562 (26 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental665 (12 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental812 (12 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental938 (10 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental1112 (6 isolates)

Schemes and loci

Tools

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