Full information on isolate SB5393 (id:4439)
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
- 4439
- isolate
- SB5393
- alias
- 821
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 20 updates show details
- date entered
- 2016-11-18
- datestamp
- 2023-01-20
- 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
- contigs
- 47
- total length
- 5,444,209 bp
- max length
- 1,041,762 bp
- mean length
- 115,835 bp
- N50
- 355,310
- L50
- 5
- N90
- 100,476
- L90
- 16
- N95
- 78,869
- L95
- 19
- %GC
- 57.23
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,362
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 | 627 | 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
- 3
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 3
- AbST
- 32-1LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi50
- K_locus
- KL52
- K_type
- K52
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.91%
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_problems
- *
- O_locus_confidence
- High
- O_locus_identity
- 94.93%
- Bla_chr
- SHV-27^
- SHV_mutations
- 156D
- iucA
- 9
- iucB
- 11
- iucC
- 12
- iucD
- 8
- iutA
- 14
Analysis performed: 2024-03-05; Kleborate v2.3.2
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 (13436 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 318 (10 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 503 (10 isolates) |
klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 318 (10 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 503 (10 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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