Full information on isolate VI9C3 (id:302)
Projects
Provenance/primary metadata
- id
- 302
- isolate
- VI9C3
- aliases
- SB2803; V9902406
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 723 updates show details
- date entered
- 2009-02-10
- datestamp
- 2025-05-29
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 1999
- city
- Mastenbroek
- country
- The Netherlands
- continent
- Europe
- source type
- Animal
- host
- Horse
- source details
- Abdomen
- infection
- Peritonitis
- source lab
- UMCU (Utrecht, NL)
- K type
- K35
Publications (2)
- 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
- 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
- 78
- total length
- 5,676,136 bp
- max length
- 296,313 bp
- mean length
- 72,771 bp
- N50
- 135,471
- L50
- 15
- N90
- 46,060
- L90
- 42
- N95
- 31,303
- L95
- 49
- %GC
- 56.83
- Ns
- 0
- gaps
- 0
- loci tagged
- 6,962
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 | 626 | 99 | |
| Kpn_cgMLST | 2752 | 2729 | 99 | |
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
- YbST
- 376
- Yersiniabactin
- ybt 14; ICEKp5
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 1
- Bla_chr
- SHV-38
- SHV_mutations
- SHV:p.Ala146Val
- 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
- wzi155
- K_locus
- KL35
- K_type
- K35
- K_locus_confidence
- Typeable
- K_locus_problems
- ?3
- K_locus_identity
- 99.52%
- O_locus
- OL3γ
- O_type
- O3γ
- O_locus_confidence
- Typeable
- O_locus_problems
- ?2
- O_locus_identity
- 99.93%
Analysis performed: 2026-01-15; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_158_22_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL45
- Clonal group
- CG10815
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_158_22_0_0 | 7 | 1 |
| 0_0_158_22_0_0_0 | 4 | 1 |
| 0_0_158_22_0_0_0_0 | 2 | 1 |
| 0_0_158_22_0_0_0_0_0 | 1 | 1 |
| 0_0_158_22_0_0_0_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_158 | 190 | 825 |
| 0_0_158_22 | 43 | 1 |
| 0_0_158_22_0 | 10 | 1 |
| 0_0_158_22_0_0 | 7 | 1 |
| 0_0_158_22_0_0_0 | 4 | 1 |
| 0_0_158_22_0_0_0_0 | 2 | 1 |
| 0_0_158_22_0_0_0_0_0 | 1 | 1 |
| 0_0_158_22_0_0_0_0_0_0 | 0 | 1 |
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 (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 | 90 (370 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 | 90 (370 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1809 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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