Full information on isolate SB6474 (id:9529)
Projects
This isolate is a member of the following project:
- Barbier et al_ApplEnvironMicrobiol_2020
- Collection of KpSC genomes studied in "The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples" (PMID: 32005732)
Provenance/primary metadata
- id
- 9529
- isolate
- SB6474
- alias
- MVK-03E157
- sender
- Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 12 updates show details
- date entered
- 2019-08-08
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Auxonne
- country
- France
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- soil
- source lab
- persil soil
- comments
- Auxonne
Sequence bin
- contigs
- 70
- total length
- 5,255,614 bp
- max length
- 379,308 bp
- mean length
- 75,081 bp
- N50
- 211,908
- L50
- 10
- N90
- 52,748
- L90
- 29
- N95
- 29,440
- L95
- 36
- %GC
- 57.78
- Ns
- 0
- gaps
- 0
- loci tagged
- 703
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 | 627 | 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
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- unknown (KL166)
- K_type
- unknown (KL166)
- K_locus_problems
- ?-*
- K_locus_confidence
- None
- K_locus_identity
- 84.71%
- K_locus_missing_genes
- KL166_02_cpsACP,KL166_03_wzi,KL166_04_wza,KL166_05_wzb,KL166_06_wzc,KL166_07,KL166_08_wzx,KL166_09_wzy,KL166_10_wcuP,KL166_11_wcuF,KL166_12_wcmY,KL166_13_wcuC,KL166_14_wcaJ,KL166_15_gnd,KL166_17_manB,KL166_18_rmlB,KL166_19_rmlA,KL166_20_rmlD,KL166_21_rmlC
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 97.99%
- O_locus_missing_genes
- O3/O3a_02_manB
- Bla_chr
- SHV-1^
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_46_5_0_1_0_0_1_0
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 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (7 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (7 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: