Full information on isolate CMKP01 (id:9640)
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
- 9640
- isolate
- CMKP01
- alias
- PJAM
- sender
- Guillaume Rollin, Beaujon hospital, Paris, France
- curator
- Auto Tagger
- update history
- 9 updates show details
- date entered
- 2019-09-03
- datestamp
- 2023-01-21
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2014
- city
- Charleville-Meziere
- country
- France
- continent
- Europe
- host
- Human
- source details
- CSF
- infection
- Meningitis
- K type
- K2
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
- contigs
- 109
- total length
- 5,564,938 bp
- max length
- 842,896 bp
- mean length
- 51,055 bp
- N50
- 672,997
- L50
- 4
- N90
- 86,489
- L90
- 13
- N95
- 39,784
- L95
- 18
- %GC
- 57.15
- Ns
- 0
- gaps
- 0
- loci tagged
- 749
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 | 625 | 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
- virulence_score
- 5
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 12; ICEKp10
- YbST
- 1-1LV
- Colibactin
- clb 1
- CbST
- 1-1LV
- 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
- 99.73%
- 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
- truncated_resistance_hits
- tetU*?-0%
- ybtS
- 1
- ybtX
- 1
- ybtQ
- 1
- ybtP
- 1
- ybtA
- 1
- irp2
- 3
- irp1
- 16*
- ybtU
- 1
- ybtT
- 1
- ybtE
- 1
- fyuA
- 1
- clbA
- 1
- clbB
- 5*
- 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: 2024-03-12; 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_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) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: