Full information on isolate HGKP01 (id:9641)
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
- 9641
- isolate
- HGKP01
- alias
- SLEO
- sender
- Guillaume Rollin, Beaujon hospital, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 8 updates show details
- date entered
- 2019-09-03
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Paris
- 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
- 96
- total length
- 5,435,221 bp
- max length
- 492,140 bp
- mean length
- 56,617 bp
- N50
- 258,172
- L50
- 8
- N90
- 49,385
- L90
- 27
- N95
- 38,960
- L95
- 33
- %GC
- 57.18
- Ns
- 0
- gaps
- 0
- loci tagged
- 702
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 | 619 | 98 | |
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
- 3
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 2
- AbST
- 3-1LV
- Salmochelin
- iro 2
- SmST
- 4-2LV
- RmpADC
- rmp 2; KpVP-2
- RmST
- 166
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.33%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_confidence
- High
- O_locus_identity
- 98.96%
- O_locus_missing_genes
- O1/O2v2_09_gmlB
- Bla_chr
- SHV-77^
- SHV_mutations
- 35Q
- iucA
- 2
- iucB
- 6
- iucC
- 5*
- iucD
- 6
- iutA
- 26
- iroB
- 4*
- iroC
- 9
- iroD
- 5
- iroN
- 9
- rmpA
- 89
- rmpD
- 32
- rmpC
- 5
Analysis performed: 2024-03-12; 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 | 412 (8 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 | 412 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 3208 (1 isolate) |
Schemes and loci
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Tools
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