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Full information on isolate hvKP1 (id:1514)

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
1514
isolate
hvKP1
sender
Suzanne Bialek, AP-HP
curator
Auto Tagger
update history
727 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
city
Buffalo
country
USA
continent
North America
source type
Human
host
Human
source details
Blood
infection
Liver abscess
accession number
AOIZ01

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
  • Russo TA, Gill SR (2013). Draft Genome Sequence of the Hypervirulent Klebsiella pneumoniae Strain hvKP1, Isolated in Buffalo, New York. Genome Announc 1:e0006513

Sequence bin

contigs
272
total length
5,368,567 bp
max length
119,943 bp
mean length
19,738 bp
N50
43,309
L50
43
N90
13,836
L90
125
N95
8,536
L95
148
%GC
57.35
Ns
9
gaps
3
loci tagged
4,018

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_S62962098

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
virulence_score
4
resistance_score
0
num_resistance_classes
1
num_resistance_genes
1
Yersiniabactin
ybt 10; ICEKp4?
YbST
72
CbST
0
Aerobactin
iuc 1
AbST
1
Salmochelin
iro 1
SmST
15
RmpADC
rmp 1; KpVP-1
RmST
26
wzi
wzi2
K_locus
KL2
K_type
K2
K_locus_problems
?-
K_locus_confidence
Good
K_locus_identity
99.93%
K_locus_missing_genes
KL2_13
O_locus
O1/O2v1
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.45%
AGly_acquired
aph3-Ia.v1^
Bla_chr
SHV-1^
ybtS
3
ybtX
10
ybtQ
4
ybtP
3
ybtA
7
irp2
5
irp1
5
ybtU
3
ybtT
10
ybtE
9
fyuA
10
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
iroB
1
iroC
1
iroD
3
iroN
1
rmpA
2
rmpD
2
rmpC
2
spurious_virulence_hits
rmpA_55*-0%;rmpA_40*-45%

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

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_395_0_13_1_0_0_0_0

Show all thresholds

PrefixThresholdMatching isolates
0_0_395_0_13_173
0_0_395_0_13_1_043
0_0_395_0_13_1_0_023
0_0_395_0_13_1_0_0_013
0_0_395_0_13_1_0_0_0_003
061037874
0_058537874
0_0_395190178
0_0_395_043169
0_0_395_0_131026
0_0_395_0_13_173
0_0_395_0_13_1_043
0_0_395_0_13_1_0_023
0_0_395_0_13_1_0_0_013
0_0_395_0_13_1_0_0_0_003

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 (13440 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13419 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental69 (56 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental425 (13 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental974 (4 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental1512 (3 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental1870 (3 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2182 (3 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental2664 (3 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13440 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13419 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental69 (56 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental425 (13 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental974 (4 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental1512 (3 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental1870 (3 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2182 (3 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental2664 (3 isolates)

Schemes and loci

Tools

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