Full information on isolate T7-348 (id:10876)
Projects
This isolate is a member of the following project:
- Raffelsberger et al 2021_GutMicrobes
- Collection of KpSC genomes studied in "Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity" (PMID: 34182896, T7 Klebsiella project)
Provenance/primary metadata
- id
- 10876
- isolate
- T7-348
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 10 updates show details
- date entered
- 2019-11-21
- datestamp
- 2024-05-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2015
- country
- Norway
- continent
- Europe
- host
- Homo sapiens
- source details
- Faeces
- comments
- ST3580-2LV
Publication (1)
- Raffelsberger N, Hetland MAK, Svendsen K, Småbrekke L, Löhr IH, Andreassen LLE, Brisse S, Holt KE, Sundsfjord A, Samuelsen Ø, Gravningen K (2021). Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. Gut Microbes 13:1939599
Sequence bin
- contigs
- 81
- total length
- 5,336,120 bp
- max length
- 800,313 bp
- mean length
- 65,879 bp
- N50
- 372,415
- L50
- 6
- N90
- 94,294
- L90
- 17
- N95
- 39,997
- L95
- 21
- %GC
- 57.38
- Ns
- 0
- gaps
- 0
- loci tagged
- 698
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: 2022-11-02
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
- wzi
- wzi24
- K_locus
- KL108
- K_type
- unknown (KL108)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.36%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.69%
- Bla_chr
- SHV-1^
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 | 1504 (1 isolate) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2509 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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