Full information on isolate KpS13 (id:1526)
Projects
Provenance/primary metadata
- id
- 1526
- isolate
- KpS13
- aliases
- Kp FLO; SB3434
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 739 updates show details
- date entered
- 2013-04-02
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0020
- isolation year
- 2004
- city
- Villejuif
- country
- France
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
- infection
- Sepsis
- other source info
- Nosocomial infection
- source lab
- Hopital Paul Brousse, AP-HP
- resistance info
- VIM-1, SHV-5, TEM-1
- K type
- K2
- K typing method
- C-pattern
Publication (1)
- 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
Sequence bin
- contigs
- 248
- total length
- 6,198,683 bp
- max length
- 227,230 bp
- mean length
- 24,995 bp
- N50
- 70,382
- L50
- 28
- N90
- 15,927
- L90
- 101
- N95
- 7,494
- L95
- 130
- %GC
- 56.56
- Ns
- 17
- gaps
- 2
- loci tagged
- 4,061
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | assembly size too large (fail threshold: 6,132,847) | |
| 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 | |
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
- 4
- resistance_score
- 2
- num_resistance_classes
- 6
- num_resistance_genes
- 7
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 178
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 1
- Salmochelin
- iro unknown,-
- SmST
- 0,0
- RmpADC
- rmp 3; ICEKp1 (truncated)
- RmST
- 32-1LV
- wzi
- wzi1
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.75%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_confidence
- High
- O_locus_identity
- 99.96%
- O_locus_missing_genes
- O1/O2v1_06_wbbO
- AGly_acquired
- aac(3)-Ia*;aac(6')-Il;aac(6')-Im
- MLS_acquired
- mphB.v1
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA1.v2
- Bla_Carb_acquired
- VIM-1
- Bla_chr
- SHV-28.v1^
- Omp_mutations
- OmpK36GD
- Flq_mutations
- GyrA-83F;GyrA-87G;ParC-84G
- truncated_resistance_hits
- aac(6')-Ib10?-0%;aadA24*?-0%
- spurious_resistance_hits
- aph(2'')-IIa*?-0%
- ybtS
- 5
- ybtX
- 11
- ybtQ
- 6
- ybtP
- 5
- ybtA
- 1
- irp2
- 16
- irp1
- 15
- ybtU
- 9
- ybtT
- 5
- ybtE
- 5
- fyuA
- 11
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 1
- iroB
- 6*,1
- iroC
- 12-4%,-
- iroD
- 7,-
- iroN
- 5,-
- rmpA
- 13-54%
- rmpD
- 5
- rmpC
- 6
- spurious_virulence_hits
- rmpA_55*-0%;rmpA_55*-45%
Analysis performed: 2024-01-29; 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 | 1 (804 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 81 (146 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 | 1 (804 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 81 (146 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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