Full information on isolate GCA_900608145.1 (id:50734)
Projects
This isolate is a member of the following project:
- Hennart_et_al_2022_full_collection
- Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230
Provenance/primary metadata
- id
- 50734
- isolate
- GCA_900608145.1
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-04-14
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- Switzerland
- continent
- Europe
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMEA4916099
Sequence bin
- contigs
- 7
- total length
- 5,591,149 bp
- max length
- 5,355,937 bp
- mean length
- 798,736 bp
- N50
- 5,355,937
- L50
- 1
- N90
- 5,355,937
- L90
- 1
- N95
- 5,355,937
- L95
- 1
- %GC
- 57.12
- Ns
- 0
- gaps
- 0
- loci tagged
- 684
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 | 624 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 4
- resistance_score
- 3
- num_resistance_classes
- 9
- num_resistance_genes
- 9
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- Aerobactin
- iuc 5
- AbST
- 61-3LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- unknown (KL51)
- K_type
- unknown (K51)
- K_locus_confidence
- None
- K_locus_identity
- 98.94%
- K_locus_missing_genes
- KL51_07_wcaJ,KL51_08_wcpB,KL51_09_wzy,KL51_10_wcuF,KL51_11_wcpA,KL51_12_wzx,KL51_13,KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- -*
- O_locus_confidence
- High
- O_locus_identity
- 98.30%
- O_locus_missing_genes
- O1/O2v2_08_gmlC
- AGly_acquired
- aac(6')-Ib;aadA2^;rmtF
- MLS_acquired
- mphA
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- OXA-232
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Col_mutations
- MgrB-15%
- Flq_mutations
- GyrA-83I;GyrA-87N;ParC-80I
- truncated_resistance_hits
- CTX-M-15*?-0%
- spurious_resistance_hits
- catA1*?-0%;catA1*?-0%
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29
- iucB
- 17
- iucC
- 28
- iucD
- 35
- iutA
- 61
Analysis performed: 2024-04-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_0_8_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 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2280 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2660 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 3251 (2 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2280 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 2660 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 3251 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
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Analysis: