Full information on isolate T7-405 (id:14884)
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
- 14884
- isolate
- T7-405
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Auto Tagger
- update history
- 9 updates show details
- date entered
- 2020-09-16
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2015
- country
- Norway
- continent
- Europe
- host
- Homo sapiens
- source details
- Faeces
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
- 79
- total length
- 5,720,272 bp
- max length
- 708,039 bp
- mean length
- 72,409 bp
- N50
- 419,865
- L50
- 6
- N90
- 86,820
- L90
- 16
- N95
- 34,261
- L95
- 21
- %GC
- 57.07
- Ns
- 0
- gaps
- 0
- loci tagged
- 732
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 | 629 | 100 | |
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
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 4; plasmid
- YbST
- 361
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi316
- K_locus
- unknown (KL6)
- K_type
- unknown (K6)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.45%
- K_locus_missing_genes
- KL6_08_wctC,KL6_09_wclU,KL6_10_wckB,KL6_11_gmd,KL6_12_wcaG,KL6_13_gmm,KL6_14_wcaI,KL6_15_wzx,KL6_16_wclT,KL6_17
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.44%
- Bla_chr
- SHV-1^
- ybtS
- 18
- ybtX
- 20
- ybtQ
- 27
- ybtP
- 18
- ybtA
- 13
- irp2
- 440
- irp1
- 38
- ybtU
- 9
- ybtT
- 8
- ybtE
- 26
- fyuA
- 35
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_398_0_6_0_0_0_0_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 | 40 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 40 (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 | 40 (8 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 40 (7 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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