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
- 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
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 3
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 2A
- AbST
- 29
- Salmochelin
- iro unknown
- SmST
- 0
- RmpADC
- rmp 2A; plasmid/chr (truncated)
- RmST
- 12-1LV
- wzi
- wzi128
- K_locus
- KL1
- K_type
- K1
- K_locus_problems
- -+
- K_locus_confidence
- Good
- K_locus_identity
- 99.40%
- K_locus_missing_genes
- KL1_18_manC
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.59%
- iucA
- 3
- iucB
- 4
- iucC
- 3
- iucD
- 3
- iutA
- 4
- iroB
- 3
- iroC
- 5-2%
- iroD
- 4
- rmpA
- 7
- rmpD
- 9
- rmpC
- 4-17%
- spurious_virulence_hits
- rmpA_91*-0%
Analysis performed: 2023-07-21; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_438_1_4_0_0_0_0_0
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 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 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 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 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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