Full information on isolate SB1139 (id:252)
Projects
Provenance/primary metadata
- id
- 252
- isolate
- SB1139
- alias
- SB1139
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 25 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
- city
- Utrecht
- country
- The Netherlands
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Faeces
- infection
- Carriage
- source lab
- UMCU (Utrecht, NL)
Publications (2)
- 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
- 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
- 45
- total length
- 5,344,906 bp
- max length
- 775,329 bp
- mean length
- 118,776 bp
- N50
- 331,189
- L50
- 6
- N90
- 101,067
- L90
- 16
- N95
- 69,476
- L95
- 19
- %GC
- 57.35
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,249
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 | 629 | 100 | |
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
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 202-4LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi8
- K_locus
- KL8
- K_type
- K8
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.85%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.43%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- ybtS
- 5
- ybtX
- 19
- ybtQ
- 102
- ybtP
- 5
- ybtA
- 1
- irp2
- 252
- irp1
- 249
- ybtU
- 66
- ybtT
- 5
- ybtE
- 5
- fyuA
- 21
Analysis performed: 2023-07-21; Kleborate v2.3.2
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 | 5 (350 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 650 (14 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 | 5 (350 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 650 (14 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 5 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 5 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 5 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 5 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 5 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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