Full information on isolate EC0519 (id:14537)
Provenance/primary metadata
- id
- 14537
- isolate
- EC0519
- alias
- 13DS021284
- sender
- Nurdyana Abdul Rahman, General Hospital, Singapore
- curator
- Auto Tagger
- update history
- 13 updates show details
- date entered
- 2020-09-02
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2013
- country
- Singapore
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Intestinal
- other source info
- Rectum clinical sample
Sequence bin
- contigs
- 194
- total length
- 5,576,274 bp
- max length
- 288,936 bp
- mean length
- 28,744 bp
- N50
- 138,555
- L50
- 15
- N90
- 20,337
- L90
- 53
- N95
- 9,351
- L95
- 72
- %GC
- 57.10
- Ns
- 0
- gaps
- 0
- loci tagged
- 706
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 | 620 | 98 | |
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
- 2
- num_resistance_genes
- 2
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 78.37%
- K_locus_missing_genes
- KL107_02_cpsACP,KL107_04_wza,KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10
- O_locus
- unknown (OL102)
- O_type
- unknown (OL102)
- O_locus_problems
- ?-+*
- O_locus_confidence
- None
- O_locus_identity
- 82.49%
- O_locus_missing_genes
- OL102_05_wbbL,OL102_06_rhamnan,OL102_07_wzm,OL102_08_wzt
- MLS_acquired
- mphA
- Bla_Carb_acquired
- KPC-2
- Bla_chr
- SHV-1^
- spurious_resistance_hits
- TEM-10.v2?-43%;TEM-117?-0%
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_659_0_0_0_0_0_0_0
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 (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 | 52 (57 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 | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2304 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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