Full information on isolate SB5379 (id:4425)
Projects
This isolate is a member of the following project:
- Huynh et al 2020 Gut Microbes
- Collection of KpSC genomes studied in "Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors" (PMID 32404021, ACIP project)
Provenance/primary metadata
- id
- 4425
- isolate
- SB5379
- alias
- 806
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
- update history
- 24 updates show details
- date entered
- 2016-11-18
- datestamp
- 2025-07-18
- taxonomic designation
- K. variicola subsp. variicola
- phylogroup from ST
- Kp3 (7 loci)
- 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
Publication (1)
- 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
- method
- Unknown
- contigs
- 72
- total length
- 5,767,679 bp
- max length
- 912,205 bp
- mean length
- 80,107 bp
- N50
- 316,215
- L50
- 6
- N90
- 86,457
- L90
- 19
- N95
- 34,630
- L95
- 24
- %GC
- 57.26
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,350
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 | 619 | 98 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella variicola | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella variicola subsp. variicola
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 5
- num_resistance_genes
- 7
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi508
- K_locus
- KL10
- K_type
- K10
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 96.33%
- K_locus_missing_genes
- KL10_11_wcuQ,KL10_12_wcaN
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.58%
- AGly_acquired
- strA.v1;strB.v1
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA5
- Bla_acquired
- TEM-1D.v1^
- Bla_chr
- LEN-16^
Analysis performed: 2025-05-14; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 1_0_15_4_2_0_0_0_0_0
- Phylogroup
- Kp3
- Sublineage
- SL595
- Clonal group
- CG906
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 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 624 (16 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1106 (5 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 624 (16 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1106 (5 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: