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Full information on isolate SA12 (id:1517)

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
1517
isolate
SA12
aliases
SA12; SB4385
sender
Suzanne Bialek, AP-HP
curator
Auto Tagger
update history
732 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
isolation year
2008
city
Paris
country
France
continent
Europe
source type
Human
host
Human
source details
Liver pus
infection
Liver abscess
K type
K1
K typing method
PCR

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
  • 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

Sequence bin

contigs
454
total length
5,531,648 bp
max length
100,753 bp
mean length
12,185 bp
N50
27,726
L50
60
N90
6,339
L90
219
N95
3,961
L95
272
%GC
57.23
Ns
0
gaps
0
loci tagged
3,972

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_S62961898

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
5
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 1; ICEKp10
YbST
337
Colibactin
clb 2
CbST
29
Aerobactin
iuc 1
AbST
1
Salmochelin
iro 1
SmST
2
RmpADC
rmp 1; KpVP-1
RmST
26
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.98%
O_locus
O1/O2v2
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.13%
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
ybtS
2
ybtX
2
ybtQ
2
ybtP
2
ybtA
2
irp2
14
irp1
6
ybtU
2
ybtT
2
ybtE
2
fyuA
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
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
iroB
1
iroC
4
iroD
1
iroN
1
rmpA
2
rmpD
2
rmpC
2
spurious_virulence_hits
rmpA_55*-0%;rmpA_40*-45%

Analysis performed: 2023-07-21; 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-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)

Schemes and loci

Tools

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