Full information on isolate SB5387 (id:4433)
Projects
Provenance/primary metadata
- id
- 4433
- isolate
- SB5387
- alias
- 814
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 26 updates show details
- date entered
- 2016-11-18
- datestamp
- 2023-01-13
- taxonomic designation
- K. variicola subsp. tropica
- phylogroup from ST
- Mixed: Kp5 (6 loci), Kp5/Kp3 (1 locus)
- QC status
- 0000
- isolation year
- 2015
- country
- Madagascar
- continent
- Africa
- host
- pregnant woman
- source details
- Fecal sample
- infection
- carriage
- source lab
- Institut Pasteur of Madagascar
Publications (2)
- Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
- Huynh BT, Passet V, Rakotondrasoa A, Diallo T, Kerleguer A, Hennart M, Lauzanne A, Herindrainy P, Seck A, Bercion R, Borand L, Pardos de la Gandara M, Delarocque-Astagneau E, Guillemot D, Vray M, Garin B, Collard JM, Rodrigues C, Brisse S (2020). Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors. Gut Microbes 11:1287-1299
Sequence bin
- contigs
- 56
- total length
- 5,698,764 bp
- max length
- 876,399 bp
- mean length
- 101,764 bp
- N50
- 279,038
- L50
- 7
- N90
- 91,682
- L90
- 20
- N95
- 46,791
- L95
- 24
- %GC
- 57.06
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,345
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 | 50 | 94 | |
| scgMLST629_S | 629 | 613 | 97 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella variicola | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola | 100% |
Analysis performed: 2022-12-01
Kleborate
- species
- Klebsiella variicola subsp. tropica
- 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
- wzi509
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 82.73%
- K_locus_missing_genes
- KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_11_gnd,KL107_12,KL107_13,KL107_15
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_problems
- ?-+*
- O_locus_confidence
- Good
- O_locus_identity
- 91.57%
- O_locus_missing_genes
- OL101_01_rfbB,OL101_02_rfbA,OL101_04_rfbC
- Bla_chr
- LEN-39
Analysis performed: 2024-03-05; 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 | 6 (21 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 6 (21 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 25 (1 isolate) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 25 (1 isolate) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 25 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 25 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 25 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 25 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 25 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 25 (1 isolate) |
Schemes and loci
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