Full information on isolate CIP 52.208 (id:308)
Projects
This isolate is a member of the following project:
- Public isolates
- This project contains the isolates that should be publicly available through the public access database.
Provenance/primary metadata
- id
- 308
- isolate
- CIP 52.208
- aliases
- A 5054; SB3178
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 664 updates show details
- date entered
- 2009-02-10
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- country
- Unknown
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- source lab
- Institut Pasteur
- K type
- K1
- K typing method
- Antiserum
- duplicate number
- 12
- comments
- K1 ref strain
Publication (1)
- 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
- 348
- total length
- 5,197,670 bp
- max length
- 225,872 bp
- mean length
- 14,936 bp
- N50
- 67,748
- L50
- 26
- N90
- 15,387
- L90
- 86
- N95
- 8,181
- L95
- 107
- %GC
- 57.28
- Ns
- 511
- gaps
- 6
- loci tagged
- 2,677
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 | 612 | 97 | |
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 | KL1 | K1 | Typeable | ! | 99.48% | 99.91% | -21 bp | 20 / 20 (100.00%) | 0 | 0 / 20 (0.00%) | 2 | KL40_05_rfaG,97.89%,99.74%;KL150_19_gmd,99.40%,100.00% | KL1_18_manC,99.02%,23.35%,truncated | ||||
| Klebsiella O locus | OL2α.1 | O1αβ,2α | Typeable | ! | 99.28% | 100.00% | 0 bp | 7 / 7 (100.00%) | 0 | 0 / 7 (0.00%) | 2 | OL3γ_01_manC,99.02%,23.35%;OL3α/β_02_manB,99.55%,97.39% | Extra_genes_wbmVWX_01_wbmV,100.00%,18.53%,truncated | Extra_genes_wbbYZ_02_wbbY,99.86%,100.00%;Extra_genes_wbbYZ_01_wbbZ,98.88%,100.00%;Extra_genes_wbmVWX_01_wbmV,100.00%,18.53%,truncated |
Klebsiella K locus
Klebsiella O locus
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
- QC_warnings
- ambiguous_bases
- YbST
- 0
- CbST
- 0
- AbST
- 29
- Aerobactin
- iuc 2A
- iucA
- 3
- iucB
- 4
- iucC
- 3
- iucD
- 3
- iutA
- 4
- SmST
- 0
- Salmochelin
- iro unknown
- iroB
- 3
- iroC
- 5-2%
- iroD
- 4
- RmST
- 12-1LV
- RmpADC
- rmp 2A; plasmid/chr (truncated)
- rmpA
- 7
- rmpD
- 9
- rmpC
- 4-17%
- virulence_score
- 3
- 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
- wzi128
- K_locus
- KL1
- K_type
- K1
- K_locus_confidence
- Typeable
- K_locus_problems
- !
- K_locus_identity
- 99.48%
- O_locus
- OL2α.1
- O_type
- O1αβ,2α
- O_locus_confidence
- Typeable
- O_locus_problems
- !
- O_locus_identity
- 99.28%
Analysis performed: 2026-01-15; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_438_1_4_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL82
- Clonal group
- CG14195
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 | 432 (14 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1196 (9 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 | 432 (14 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1196 (9 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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