Full information on isolate KP_NORM_URN_100419 (id:10415)
Provenance/primary metadata
- id
- 10415
- isolate
- KP_NORM_URN_100419
- alias
- KP_NORM_URN_2014_100419
- sender
- Marit Andrea Klokkhammer Hetland, Stavanger University Hospital, Department of Medical Microbiology, Norway
- curator
- Auto Tagger
- update history
- 11 updates show details
- embargo history
- show details
- date entered
- 2019-10-16
- datestamp
- 2025-05-29
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2014
- country
- Norway
- continent
- Europe
- host
- Homo sapiens
- source details
- Urine
- resistance info
- ESBL
Sequence bin
- method
- Illumina
- contigs
- 85
- total length
- 5,504,127 bp
- max length
- 965,145 bp
- mean length
- 64,755 bp
- N50
- 338,227
- L50
- 6
- N90
- 94,247
- L90
- 17
- N95
- 34,195
- L95
- 23
- %GC
- 57.21
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,459
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 53 | 100 | |
| scgMLST629_S | 629 | 626 | 99 | |
| Kpn_cgMLST | 2752 | 2735 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-11-02
Kaptive
| Database | Best match locus | Best match type | Match confidence | Problems | Identity | Coverage | Length discrepancy | Expected genes in locus | Missing expected genes | Other genes in locus | Other genes in locus, details | Expected genes outside locus | Expected genes outside locus, details | Other genes outside locus | Other genes outside locus, details | Truncated genes, details | Extra genes, details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Klebsiella K locus | KL51 | K51 | Typeable | ! | 99.69% | 99.99% | 3 bp | 16 / 16 (100.00%) | 0 | 0 / 16 (0.00%) | 4 | KL40_03_wcpO,98.99%,100.00%;KL40_04,99.75%,100.00%;KL40_05_rfaG,99.47%,100.00%;KL150_19_gmd,98.80%,100.00% | KL51_14_wcoZ,100.00%,24.15%,truncated | ||||
| Klebsiella O locus | OL2α.2 | O1αβ,2β | Typeable | ! | 99.21% | 99.82% | -14 bp | 7 / 7 (100.00%) | 0 | 0 / 7 (0.00%) | 0 | OL2α.2_04_glf,99.24%,36.20%,truncated | Extra_genes_wbbYZ_02_wbbY,99.86%,100.00%;Extra_genes_gml2β_03_gmlC,97.12%,100.00%;Extra_genes_gml2β_02_gmlB,99.39%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.26%,100.00%;Extra_genes_gml2β_01_gmlA,99.20%,100.00% |
Klebsiella K locus
Klebsiella O locus
Analysis performed: 2026-03-14; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- YbST
- 437
- Yersiniabactin
- ybt 14; ICEKp5
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 31
- ybtP
- 4
- ybtA
- 1
- irp2
- 67
- irp1
- 449
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 36
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 1
- AGly_acquired
- strB.v1;strA.v1^;aac(6')-Ib-cr.v2
- Flq_acquired
- aac(6')-Ib-cr.v2
- Sul_acquired
- sul2*
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- Flq_mutations
- GyrA:p.Ser83Ile;ParC:p.Ser80Ile
- truncated_resistance_hits
- TEM-206?-0%
- spurious_resistance_hits
- catB3.v1?-70%
- resistance_score
- 1
- num_resistance_classes
- 6
- num_resistance_genes
- 8
- Ciprofloxacin_prediction
- nonwildtype R
- Ciprofloxacin_profile_support
- 99.21% R (N=2147/2167)
- Ciprofloxacin_profile
- >1 QRDR, 0 PMQR, * aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 2 mg/L [2-4]
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_confidence
- Typeable
- K_locus_problems
- !
- K_locus_identity
- 99.69%
- O_locus
- OL2α.2
- O_type
- O1αβ,2β
- O_locus_confidence
- Typeable
- O_locus_problems
- !
- O_locus_identity
- 99.21%
Analysis performed: 2026-03-14; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_17_0_2_0
- Phylogroup
- Kp1
- Sublineage
- SL231
- Clonal group
- CG231
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (97 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (90 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (97 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (90 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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