Full information on isolate SB5376 (id:4422)
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
- 4422
- isolate
- SB5376
- alias
- 789
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 20 updates show details
- date entered
- 2016-11-18
- datestamp
- 2025-05-29
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (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
- 55
- total length
- 5,330,747 bp
- max length
- 921,206 bp
- mean length
- 96,923 bp
- N50
- 338,002
- L50
- 6
- N90
- 86,409
- L90
- 18
- N95
- 56,829
- L95
- 21
- %GC
- 57.47
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,098
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 | 628 | 99 | |
| Kpn_cgMLST | 2752 | 2741 | 99 | |
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
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi97
- K_locus
- KL46
- K_type
- K46
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.99%
- K_locus_missing_genes
- KL46_12_wcuF
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.21%
- Bla_chr
- SHV-119^
- SHV_mutations
- 35Q
Analysis performed: 2024-03-05; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_1049_0_0_0_0_0_1_0
- Phylogroup
- Kp1
- Sublineage
- SL10914
- Clonal group
- CG11644
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_1049_0_0_0 | 7 | 3 |
| 0_0_1049_0_0_0_0 | 4 | 3 |
| 0_0_1049_0_0_0_0_0 | 2 | 3 |
| 0_0_1049_0_0_0_0_0_1 | 1 | 2 |
| 0_0_1049_0_0_0_0_0_1_0 | 0 | 2 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_1049 | 190 | 3 |
| 0_0_1049_0 | 43 | 3 |
| 0_0_1049_0_0 | 10 | 3 |
| 0_0_1049_0_0_0 | 7 | 3 |
| 0_0_1049_0_0_0_0 | 4 | 3 |
| 0_0_1049_0_0_0_0_0 | 2 | 3 |
| 0_0_1049_0_0_0_0_0_1 | 1 | 2 |
| 0_0_1049_0_0_0_0_0_1_0 | 0 | 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 (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 | 1611 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2737 (3 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 | 1611 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2737 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: