Full information on isolate K45-67 (id:213)
Projects
Provenance/primary metadata
- id
- 213
- isolate
- K45-67
- sender
- Christian Giske, Karolinska University Hospital, Solna, Sweden
- curator
- Auto Tagger
- update history
- 19 updates show details
- date entered
- 2008-09-05
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2007
- city
- Tromso
- country
- Norway
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Publication (1)
- Samuelsen Ø, Toleman MA, Hasseltvedt V, Fuursted K, Leegaard TM, Walsh TR, Sundsfjord A, Giske CG (2011). Molecular characterization of VIM-producing Klebsiella pneumoniae from Scandinavia reveals genetic relatedness with international clonal complexes encoding transferable multidrug resistance. Clin Microbiol Infect 17:1811-6
Sequence bin
- contigs
- 417
- total length
- 5,415,345 bp
- max length
- 282,129 bp
- mean length
- 12,987 bp
- N50
- 70,221
- L50
- 23
- N90
- 9,619
- L90
- 111
- N95
- 5,014
- L95
- 149
- %GC
- 57.14
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,148
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 | 609 | 96 | |
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
- 2
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi174
- K_locus
- KL74
- K_type
- K74
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 98.94%
- K_locus_missing_genes
- KL74_18_manB
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- ?-*
- O_locus_confidence
- Good
- O_locus_identity
- 91.68%
- O_locus_missing_genes
- O3b_02_manB
- AGly_acquired
- aac(6')-Ib4^;aadA2^;aph3-Ia.v1^;strA.v1;strB.v1
- MLS_acquired
- mphA
- Phe_acquired
- catII.2*
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12;dfrA14.v2*
- Bla_Carb_acquired
- VIM-1
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- qnrS1?-87%
- spurious_resistance_hits
- SHV-12?-0%
Analysis performed: 2023-07-21; 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 | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 347 (18 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 273 (13 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 668 (7 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2083 (3 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2429 (3 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 2957 (3 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 | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 347 (18 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 273 (13 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 668 (7 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2083 (3 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2429 (3 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 2957 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: