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Full information on isolate A5011 (id:397)

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
397
isolate
A5011
aliases
A5011; SB3927
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
729 updates show details
date entered
2009-02-10
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
city
Taiwan
country
Taiwan
continent
Asia
source type
Human
host
Human
source details
Liver pus
infection
Liver abscess
source lab
Taiwan Univ. College of Medicine

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

contigs
436
total length
5,406,580 bp
max length
82,222 bp
mean length
12,401 bp
N50
22,496
L50
76
N90
6,004
L90
260
N95
4,448
L95
312
%GC
57.38
Ns
0
gaps
0
loci tagged
3,890

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_S62960395

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
2
resistance_score
0
num_resistance_classes
1
num_resistance_genes
0
Yersiniabactin
ybt 1; ICEKp10 (truncated)
YbST
47-1LV
Colibactin
clb 2 (incomplete) (truncated)
CbST
27-3LV
AbST
0
Salmochelin
iro 1
SmST
2
RmpADC
rmp 1; KpVP-1
RmST
26
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_problems
?-
K_locus_confidence
Good
K_locus_identity
99.99%
K_locus_missing_genes
KL1_06_wzc
O_locus
O1/O2v2
O_type
O1
O_locus_problems
?-
O_locus_confidence
Good
O_locus_identity
99.11%
O_locus_missing_genes
O1/O2v2_08_gmlC,O1/O2v2_09_gmlB
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
Col_mutations
PmrB-43%
ybtS
2
ybtX
2*-0%
ybtQ
2
ybtP
2
ybtA
2
irp2
6
irp1
6
ybtU
2
ybtT
2
ybtE
2
fyuA
2
clbA
3
clbB
2
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
3
clbI
2
clbL
2*-0%
clbM
2
clbN
2
clbP
2
clbQ
2
iroB
1
iroC
4
iroD
1
iroN
1
rmpA
2
rmpD
2
rmpC
2
spurious_virulence_hits
clbO_13*-0%

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

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