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Full information on isolate BJ1-GA (id:1509)

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)
Hennart et al. 2022_MBE
Reference Genomes for LINcodes (Table S9) (PMID: 35700230)

Provenance/primary metadata

id
1509
isolate
BJ1-GA
alias
SB4496
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
731 updates show details
date entered
2013-03-25
datestamp
2025-05-29
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2011
city
Clichy
country
France
continent
Europe
source type
Human
host
Human
source details
Liver pus
infection
Liver abscess
source lab
MHNC, Hopital Beaujon, AP-HP
K type
K2

Publications (4)

  • 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
  • Bialek-Davenet S, Nicolas-Chanoine MH, Decré D, Brisse S (2013). Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea. Epidemiol Infect 141:188
  • 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
  • Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:

Sequence bin

method
Illumina
contigs
114
total length
5,421,195 bp
max length
253,983 bp
mean length
47,555 bp
N50
133,474
L50
15
N90
29,159
L90
50
N95
20,102
L95
62
%GC
57.30
Ns
0
gaps
0
loci tagged
6,758

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_S62962499
Kpn_cgMLST2752269998

Analysis

rMLST species identification

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

Analysis performed: 2022-12-01

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
5
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 12; ICEKp10
YbST
1
Colibactin
clb 1
CbST
1
Aerobactin
iuc 2
AbST
14
Salmochelin
iro 2
SmST
3
RmpADC
rmp 2; KpVP-2
RmST
7
wzi
wzi2
K_locus
KL2
K_type
K2
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.74%
O_locus
O1/O2v1
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.95%
Bla_chr
SHV-207
ybtS
1
ybtX
1
ybtQ
1
ybtP
1
ybtA
1
irp2
3
irp1
3
ybtU
1
ybtT
1
ybtE
1
fyuA
1
clbA
1
clbB
1
clbC
1
clbD
1
clbE
1
clbF
1
clbG
1
clbH
1
clbI
1
clbL
1
clbM
1
clbN
1
clbO
1
clbP
1
clbQ
1
iucA
2
iucB
2
iucC
2
iucD
2
iutA
2
iroB
2
iroC
3
iroD
2
iroN
2
rmpA
3
rmpD
6
rmpC
5
spurious_virulence_hits
rmpA_91*-0%

Analysis performed: 2025-10-17; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_339_1_0_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL380
Clonal group
CG10118

Show all thresholds

PrefixThresholdMatching isolates
0_0_339_1_0_073
0_0_339_1_0_0_043
0_0_339_1_0_0_0_023
0_0_339_1_0_0_0_0_012
0_0_339_1_0_0_0_0_0_002
061041312
0_058541312
0_0_33919038
0_0_339_14321
0_0_339_1_0103
0_0_339_1_0_073
0_0_339_1_0_0_043
0_0_339_1_0_0_0_023
0_0_339_1_0_0_0_0_012
0_0_339_1_0_0_0_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-linkage190experimental11 (22 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental11 (15 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental11 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental11 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental11 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental11 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental11 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental11 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental11 (22 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental11 (15 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental11 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental11 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental11 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental11 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental11 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental11 (2 isolates)

Schemes and loci

Tools

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