Full information on isolate SAKP01 (id:9639)
Projects
This isolate is a member of the following project:
- Rollin et al 2022_IJID
- Collection of K. pneumoniae genomes studied in "Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities" (PMID: 34767984)
Provenance/primary metadata
- id
- 9639
- isolate
- SAKP01
- alias
- SA56
- sender
- Guillaume Rollin, Beaujon hospital, Paris, France
- curator
- Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
- update history
- 10 updates show details
- date entered
- 2019-09-03
- datestamp
- 2026-02-12
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2011
- city
- Paris
- country
- France
- continent
- Europe
- host
- Human
- source details
- CSF
- infection
- Meningitis
- K type
- K1
Publication (1)
- Rollin G, Rossi B, Brisse S, Decré D, Leflon-Guibout V, Bert F, Hoffmann I, Decousser JW, Fantin B, Lefort A (2022). Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities. Int J Infect Dis 114:185-191
Sequence bin
- method
- Illumina
- contigs
- 381
- total length
- 5,894,075 bp
- max length
- 341,192 bp
- mean length
- 15,471 bp
- N50
- 203,744
- L50
- 11
- N90
- 26,221
- L90
- 41
- N95
- 3,659
- L95
- 79
- %GC
- 56.88
- Ns
- 0
- gaps
- 0
- loci tagged
- 793
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: 2022-11-02
Kaptive
| Database | Best match locus | Best match type | Match confidence | Problems | Identity | Coverage | Length discrepancy | Expected genes in locus | Missing expected genes | Other genes in locus | Other genes in locus, details | Expected genes outside locus | Expected genes outside locus, details | Other genes outside locus | Other genes outside locus, details | Truncated genes, details | Extra genes, details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Klebsiella K locus | KL1 | K1 | Typeable | 99.99% | 100.00% | 0 bp | 20 / 20 (100.00%) | 0 | 0 / 20 (0.00%) | 19 | KL40_03_wcpO,97.97%,100.00%;KL2_06_wzc,99.57%,64.40%,partial;KL2_12,99.55%,76.86%,partial;KL40_04,99.50%,100.00%;KL2_04_wza,100.00%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00%;KL2_14_wcaJ,97.40%,16.56%,partial;KL2_11_wzx,99.12%,46.80%,partial;KL2_07,100.00%,42.74%,partial;KL2_08,100.00%,36.46%,partial;KL2_09,100.00%,32.99%,partial;KL2_12,96.77%,21.42%,partial;KL2_10,100.00%,26.34%,partial;KL2_06_wzc,100.00%,13.85%,partial;KL136_03_wzi,100.00%,20.96%,partial;KL2_13,100.00%,33.78%,partial;KL2_11_wzx,100.00%,7.63%,partial;KL2_08,100.00%,8.58%,partial | ||||||
| Klebsiella O locus | OL2α.2 | O1αβ,2β | Typeable | 99.29% | 100.00% | -2 bp | 7 / 7 (100.00%) | 0 | 0 / 7 (0.00%) | 4 | OL3γ_01_manC,99.58%,100.00%;OL3α/β_02_manB,99.78%,97.39%;OL2α.1_07_kfoC,97.06%,46.58%,partial;OL2α.1_07_kfoC,99.50%,46.12%,partial | Extra_genes_wbbYZ_02_wbbY,100.00%,100.00%;Extra_genes_gml2β_03_gmlC,98.56%,100.00%;Extra_genes_gml2β_02_gmlB,99.69%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00% |
Klebsiella K locus
Klebsiella O locus
Analysis performed: 2025-12-28; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- YbST
- 47
- Yersiniabactin
- ybt 1; ICEKp10
- ybtS
- 2
- ybtX
- 2
- ybtQ
- 2
- ybtP
- 2
- ybtA
- 2
- irp2
- 6
- irp1
- 6
- ybtU
- 2
- ybtT
- 2
- ybtE
- 2
- fyuA
- 2
- CbST
- 29
- Colibactin
- clb 2
- clbA
- 2
- clbB
- 2
- clbC
- 2
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 3
- clbI
- 2
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbO
- 2
- clbP
- 2
- clbQ
- 2
- AbST
- 1
- Aerobactin
- iuc 1
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 1
- SmST
- 2
- Salmochelin
- iro 1
- iroB
- 1
- iroC
- 4
- iroD
- 1
- iroN
- 1
- RmST
- 61-2LV
- RmpADC
- rmp 1; KpVP-1 (truncated)
- rmpA
- 40*-54%
- rmpD
- 2
- rmpC
- 2*-0%
- virulence_score
- 5
- Bla_chr
- SHV-11^
- SHV_mutations
- SHV:p.Leu35Gln
- 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
- wzi1
- K_locus
- KL1
- K_type
- K1
- K_locus_confidence
- Typeable
- K_locus_identity
- 99.99%
- O_locus
- OL2α.2
- O_type
- O1αβ,2β
- O_locus_confidence
- Typeable
- O_locus_identity
- 99.29%
Analysis performed: 2025-12-28; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_429_0_5_0_2_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL23
- Clonal group
- CG23
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 (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 | 6 (185 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 6 (185 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 | 6 (185 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 6 (185 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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