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Full information on isolate 100519185 (id:1513)

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
1513
isolate
100519185
alias
SB4360
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
725 updates show details
date entered
2013-03-28
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2010
city
Pau
country
France
continent
Europe
source type
Human
host
Human
source details
Blood
infection
Severe Sepsis

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

contigs
201
total length
5,356,115 bp
max length
146,877 bp
mean length
26,648 bp
N50
48,568
L50
37
N90
14,015
L90
114
N95
9,488
L95
137
%GC
57.24
Ns
0
gaps
0
loci tagged
3,999

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_S62961697

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
virulence_score
4
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 22; ICEKp12 (incomplete)
YbST
13-2LV
CbST
0
Aerobactin
iuc 1 (incomplete)
AbST
1-1LV
Salmochelin
iro 1
SmST
1-1LV
RmpADC
rmp 1; KpVP-1 (incomplete)
RmST
26-1LV
wzi
wzi2
K_locus
KL2
K_type
K2
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.93%
O_locus
O1/O2v1
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.46%
Bla_chr
SHV-1^
ybtS
11
ybtX
9
ybtQ
11
ybtP
8
ybtA
1
irp2
2
ybtU
8
ybtT
9
ybtE
8
fyuA
9
iucA
1
iucB
1
iucD
1
iutA
1
iroB
5
iroC
1
iroD
1
iroN
1
rmpD
2
rmpC
2
spurious_virulence_hits
irp1_2*-0%;irp1_245*-0%;iucC_1*-0%;rmpA_51*-0%;rmpA_88*-51%

Analysis performed: 2024-01-29; Kleborate v2.3.2

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 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental69 (56 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental69 (56 isolates)

Schemes and loci

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