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Full information on isolate A3021 (id:396)

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.
Bialek et al 2014_EID
167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)
Isolates Excluded (failed QC)
KlebNET-GSP qc

Provenance/primary metadata

id
396
isolate
A3021
aliases
A3021; SB3926
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history
727 updates show details
date entered
2009-02-10
datestamp
2022-11-03
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0100
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
K type
K1

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

method
Illumina
contigs
848
total length
5,478,137 bp
max length
41,972 bp
mean length
6,461 bp
N50
10,408
L50
163
N90
3,025
L90
527
N95
2,168
L95
634
%GC
57.33
Ns
0
gaps
0
loci tagged
2,467

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigstoo many contigs (fail threshold: 501)
Assembly size
Minimum N50N50 too low (warn threshold: 20,000)
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST535196
scgMLST629_S62955287

Analysis

rMLST species identification

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

Analysis performed: 2022-11-02

Kaptive

Database Best match locusBest match typeMatch confidenceProblemsIdentityCoverageLength discrepancyExpected genes in locusMissing expected genesOther genes in locusOther genes in locus, detailsExpected genes outside locusExpected genes outside locus, detailsOther genes outside locusOther genes outside locus, detailsTruncated genes, detailsExtra genes, details
Klebsiella K locus KL1 K1 Typeable ?2 99.99% 100.13% n/a 20 / 20 (100.00%) 0 0 / 20 (0.00%) 4 KL40_03_wcpO,97.97%,100.00%;KL40_04,99.50%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00%
Klebsiella O locus OL2α.2 O1αβ,2β Typeable 99.29% 100.00% -2 bp 7 / 7 (100.00%) 0 0 / 7 (0.00%) 2 OL3γ_01_manC,99.58%,100.00%;OL3α/β_02_manB,99.78%,97.39% Extra_genes_wbbYZ_02_wbbY,100.00%,78.51%,partial;Extra_genes_gml2β_03_gmlC,98.56%,100.00%;Extra_genes_gml2β_02_gmlB,99.69%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00%

Klebsiella K locus

2025-12-28T18:57:15.579631 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T18:57:20.008433 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Analysis performed: 2025-12-28; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.

Kleborate

species
Klebsiella pneumoniae
species_match
strong
YbST
332-2LV
Yersiniabactin
ybt 2; ICEKp1 (truncated)
ybtS
8
ybtX
7*-0%
ybtQ
9
ybtP
6
ybtA
5
irp2
13
irp1
165*-50%
ybtU
6
ybtT
7
ybtE
7
fyuA
6
spurious_ybt_hits
ybtX_138*-0%;irp1_533*-51%;irp1_533*-0%
CbST
0
AbST
17
Aerobactin
iuc 1
iucA
6
iucB
1
iucC
6
iucD
1
iutA
1
SmST
0
Salmochelin
iro unknown
iroB
6*-0%
iroD
1*-0%
iroN
1*-81%
spurious_smst_hits
iroB_23*-0%;iroB_27*-0%;iroB_31*-0%;iroD_12*-0%;iroD_17*-0%;iroD_18*-0%;iroD_21*-0%;iroD_22*-0%;iroD_25*-0%
RmST
32
RmpADC
rmp 3; ICEKp1
rmpA
11
rmpD
5
rmpC
6
virulence_score
4
spurious_virulence_hits
ybtX_138*0%;irp1_533*51%;irp1_533*0%iroB_23*0%;iroB_27*0%;iroB_31*0%;iroD_12*0%;iroD_17*0%;iroD_18*0%;iroD_21*0%;iroD_22*0%;iroD_25*0%
Bla_chr
SHV-11^
SHV_mutations
SHV:p.Leu35Gln
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Ciprofloxacin_prediction
wildtype S
Ciprofloxacin_profile_support
90.99% S (N=5168/5680)
Ciprofloxacin_profile
0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
Ciprofloxacin_MIC_prediction
0.25 mg/L [0.25-0.25]
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_confidence
Typeable
K_locus_problems
?2
K_locus_identity
99.99%
O_locus
OL2α.2
O_type
O1αβ,2β
O_locus_confidence
Typeable
O_locus_identity
99.29%

Analysis performed: 2025-12-28; Kleborate v3.2.4

Schemes and loci

Tools

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