Full information on isolate SB6440 (id:9502)
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
- 9502
- isolate
- SB6440
- alias
- MVK-03E093
- 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
- 14 updates show details
- date entered
- 2019-08-08
- datestamp
- 2023-01-13
- 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
- 58
- total length
- 5,135,240 bp
- max length
- 541,648 bp
- mean length
- 88,539 bp
- N50
- 272,426
- L50
- 7
- N90
- 65,605
- L90
- 22
- N95
- 42,862
- L95
- 27
- %GC
- 57.63
- Ns
- 0
- gaps
- 0
- loci tagged
- 700
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 | 628 | 99 |
Analysis
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-12-23
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
- wzi
- wzi180
- K_locus
- unknown (KL116)
- K_type
- unknown (KL116)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.43%
- K_locus_missing_genes
- KL116_07_wcuE,KL116_08_wckV,KL116_09,KL116_10_wctD,KL116_11_wbaZ,KL116_12_wbaP,KL116_13_wcuC,KL116_14_wzy
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.57%
- Bla_chr
- SHV-27
- SHV_mutations
- 156D
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 | 425 (4 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 713 (4 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 | 425 (4 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 713 (4 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: