Full information on isolate CIP 52.235 (id:366)
Projects
Provenance/primary metadata
- id
- 366
- isolate
- CIP 52.235
- aliases
- CIP 52.235; SB3269
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 54 updates show details
- date entered
- 2009-02-10
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Mixed: Kp1 (6 loci), Kp4 (1 locus)
- QC status
- 0100
- country
- Unknown
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- source lab
- Institut Pasteur
- K type
- K30
- K typing method
- Antiserum
- comments
- K30 ref strain
Publication (1)
- 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
- 562
- total length
- 5,349,064 bp
- max length
- 145,125 bp
- mean length
- 9,518 bp
- N50
- 29,343
- L50
- 54
- N90
- 6,118
- L90
- 211
- N95
- 3,463
- L95
- 268
- %GC
- 57.10
- Ns
- 12618
- gaps
- 128
- loci tagged
- 3,855
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| 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
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi30
- K_locus
- KL30
- K_type
- K30
- K_locus_problems
- ?-+
- K_locus_confidence
- Good
- K_locus_identity
- 99.59%
- K_locus_missing_genes
- KL30_18_manC
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.80%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
Analysis performed: 2025-05-08; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_83_6_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL43
- Clonal group
- CG12447
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 | 156 (35 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 | 156 (35 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 3648 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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