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Full information on isolate GCA_900636315.1 (id:46771)

Projects

This isolate is a member of the following project:

Hennart_et_al_2022_full_collection
Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230

Provenance/primary metadata

id
46771
isolate
GCA_900636315.1
alias
NCTC9644
sender
Mélanie Hennart, Institut Pasteur, France
curator
Auto Tagger
update history
3 updates show details
date entered
2023-03-23
datestamp
2023-03-24
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
isolation year
0
city
Unknown
country
Unknown
source type
Unknown
host
Unknown
source details
Unknown
accession number
SAMEA3492652

Sequence bin

method
Unknown
contigs
5
total length
5,809,354 bp
max length
5,457,304 bp
mean length
1,161,871 bp
N50
5,457,304
L50
1
N90
5,457,304
L90
1
N95
224,165
L95
2
%GC
57.02
Ns
0
gaps
0
loci tagged
699

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_S62962599

Analysis

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 Capsule null Typeable ! 99.66% 100.01% 2 bp 20 / 20 (100.00%) 0 0 / 20 (0.00%) 4 KL40_03_wcpO,97.77%,100.00%;KL40_04,99.25%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00% KL1_07_wzx,100.00%,23.31%,truncated;KL1_16_wcaJ,93.94%,9.42%,truncated
Klebsiella O locus OL2α.2 O1αβ,2β Typeable ! 99.25% 100.01% 0 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% OL2α.2_02_wzt,99.53%,91.87%,truncated Extra_genes_wbbYZ_02_wbbY,100.00%,100.00%;Extra_genes_gml2β_03_gmlC,98.35%,100.00%;Extra_genes_gml2β_02_gmlB,99.39%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00%

Klebsiella K locus

2025-12-28T20:11:20.861721 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-28T20:11:25.150234 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
0
CbST
0
AbST
1
Aerobactin
iuc 1
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
SmST
2
Salmochelin
iro 1
iroB
1
iroC
4
iroD
1
iroN
1
RmST
26
RmpADC
rmp 1; KpVP-1
rmpA
2
rmpD
2
rmpC
2
virulence_score
3
rmpA2
rmpA2_6*-55%
Sul_acquired
sul2
Bla_chr
SHV-11^
SHV_mutations
SHV:p.Leu35Gln
resistance_score
0
num_resistance_classes
1
num_resistance_genes
1
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
Capsule null
K_locus_confidence
Typeable
K_locus_problems
!
K_locus_identity
99.66%
O_locus
OL2α.2
O_type
O1αβ,2β
O_locus_confidence
Typeable
O_locus_problems
!
O_locus_identity
99.25%

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

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_429_0_22_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL23
Clonal group
CG23

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_22_071
0_0_429_0_22_0_041
0_0_429_0_22_0_0_021
0_0_429_0_22_0_0_0_011
0_0_429_0_22_0_0_0_0_001
061041312
0_058541312
0_0_429190492
0_0_429_043490
0_0_429_0_22101
0_0_429_0_22_071
0_0_429_0_22_0_041
0_0_429_0_22_0_0_021
0_0_429_0_22_0_0_0_011
0_0_429_0_22_0_0_0_0_001

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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-linkage190experimental6 (185 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (185 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (185 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (185 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental43 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental45 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental46 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental47 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental48 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental48 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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