Full information on isolate BJ1-GA (id:1509)
Projects
Provenance/primary metadata
- id
- 1509
- isolate
- BJ1-GA
- alias
- SB4496
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 729 updates show details
- date entered
- 2013-03-25
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2011
- city
- Clichy
- country
- France
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Liver pus
- infection
- Liver abscess
- source lab
- MHNC, Hopital Beaujon, AP-HP
- K type
- K2
Publications (4)
- 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
- Bialek-Davenet S, Nicolas-Chanoine MH, Decré D, Brisse S (2013). Microbiological and clinical characteristics of bacteraemia caused by the hypermucoviscosity phenotype of Klebsiella pneumoniae in Korea. Epidemiol Infect 141:188
- 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
- Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
Sequence bin
- contigs
- 114
- total length
- 5,421,195 bp
- max length
- 253,983 bp
- mean length
- 47,555 bp
- N50
- 133,474
- L50
- 15
- N90
- 29,159
- L90
- 50
- N95
- 20,102
- L95
- 62
- %GC
- 57.30
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,059
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 | 624 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-12-01
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 5
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 12; ICEKp10
- YbST
- 1
- Colibactin
- clb 1
- CbST
- 1
- Aerobactin
- iuc 2
- AbST
- 14
- Salmochelin
- iro 2
- SmST
- 3
- RmpADC
- rmp 2; KpVP-2
- RmST
- 7
- wzi
- wzi2
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.74%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.95%
- Bla_chr
- SHV-207
- ybtS
- 1
- ybtX
- 1
- ybtQ
- 1
- ybtP
- 1
- ybtA
- 1
- irp2
- 3
- irp1
- 3
- ybtU
- 1
- ybtT
- 1
- ybtE
- 1
- fyuA
- 1
- clbA
- 1
- clbB
- 1
- clbC
- 1
- clbD
- 1
- clbE
- 1
- clbF
- 1
- clbG
- 1
- clbH
- 1
- clbI
- 1
- clbL
- 1
- clbM
- 1
- clbN
- 1
- clbO
- 1
- clbP
- 1
- clbQ
- 1
- iucA
- 2
- iucB
- 2
- iucC
- 2
- iucD
- 2
- iutA
- 2
- iroB
- 2
- iroC
- 3
- iroD
- 2
- iroN
- 2
- rmpA
- 3
- rmpD
- 6
- rmpC
- 5
- spurious_virulence_hits
- rmpA_91*-0%
Analysis performed: 2023-07-21; 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 | 11 (19 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 11 (12 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 11 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 11 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 11 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 11 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 11 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 11 (2 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 | 11 (19 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 11 (12 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 11 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 11 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 11 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 11 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 11 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 11 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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