Full information on isolate CIP 52.145 (id:381)
Projects
Provenance/primary metadata
- id
- 381
- isolate
- CIP 52.145
- aliases
- B 5055; SB3341
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 733 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
- isolation year
- 1935
- city
- Java
- country
- Indonesia
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Unknown
- source lab
- Institut Pasteur
- K type
- K2
- K typing method
- Antiserum
- duplicate number
- 4
- comments
- K2 ref strain
Publications (3)
- 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
- Blin C, Passet V, Touchon M, Rocha EPC, Brisse S (2017). Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 19:1881-1898
- 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
- 3
- total length
- 5,656,097 bp
- max length
- 5,439,142 bp
- mean length
- 1,885,366 bp
- N50
- 5,439,142
- L50
- 1
- N90
- 5,439,142
- L90
- 1
- N95
- 5,439,142
- L95
- 1
- %GC
- 57.09
- Ns
- 4
- gaps
- 3
- loci tagged
- 4,170
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 | 618 | 98 | |
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
- 5
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 12; ICEKp10
- YbST
- 315
- Colibactin
- clb 1
- CbST
- 9-1LV
- Aerobactin
- iuc 2
- AbST
- 24
- Salmochelin
- iro 2
- SmST
- 22
- RmpADC
- rmp 2; KpVP-2
- RmST
- 2
- wzi
- wzi4
- K_locus
- KL2
- K_type
- K2
- K_locus_confidence
- High
- K_locus_identity
- 98.32%
- K_locus_missing_genes
- KL2_07,KL2_13
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.96%
- ybtS
- 7
- ybtX
- 1
- ybtQ
- 1
- ybtP
- 1
- ybtA
- 1
- irp2
- 3
- irp1
- 13
- ybtU
- 1
- ybtT
- 1
- ybtE
- 1
- fyuA
- 1
- clbA
- 1
- clbB
- 4
- clbC
- 1
- clbD
- 1
- clbE
- 1
- clbF
- 1
- clbG
- 1*
- clbH
- 5
- clbI
- 1
- clbL
- 1
- clbM
- 1
- clbN
- 1
- clbO
- 1
- clbP
- 1
- clbQ
- 1
- iucA
- 2
- iucB
- 6
- iucC
- 5
- iucD
- 6
- iutA
- 8
- iroB
- 4
- iroC
- 9
- iroD
- 5
- iroN
- 4
- rmpA
- 9
- rmpD
- 32
- rmpC
- 5
- spurious_virulence_hits
- rmpA_91*-0%
Analysis performed: 2024-02-17; Kleborate v2.3.2
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 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 412 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 695 (7 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 412 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 695 (7 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: