Full information on isolate SB6166 (id:8752)
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
- 8752
- isolate
- SB6166
- alias
- MedVetKlebs52
- 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
- 13 updates show details
- date entered
- 2019-06-05
- 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
- other source info
- Culture field of salad
- source lab
- INRA-Dijon
- comments
- Auxonne
Sequence bin
- contigs
- 53
- total length
- 5,308,651 bp
- max length
- 937,478 bp
- mean length
- 100,164 bp
- N50
- 227,501
- L50
- 6
- N90
- 59,706
- L90
- 23
- N95
- 34,427
- L95
- 28
- %GC
- 57.56
- Ns
- 0
- gaps
- 0
- loci tagged
- 727
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 | 96% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 15; ICEKp11 (incomplete)
- YbST
- 378-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi30
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 88.04%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_14,KL107_15
- O_locus
- unknown (O3/O3a)
- O_type
- unknown (O3/O3a)
- O_locus_confidence
- None
- O_locus_identity
- 98.56%
- O_locus_missing_genes
- O3/O3a_03_wzm,O3/O3a_04_wzt,O3/O3a_05_wbdD,O3/O3a_06_wbdA,O3/O3a_07_wbdB,O3/O3a_08_wbdC
- Bla_chr
- SHV-194
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 22
- ybtP
- 4
- ybtA
- 1
- irp2
- 37*
- irp1
- 44
- ybtU
- 14
- ybtT
- 1
- ybtE
- 4
- spurious_virulence_hits
- fyuA_17*-72%
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_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 | 1020 (1 isolate) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1721 (1 isolate) |
Schemes and loci
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Tools
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