Full information on isolate SB5391 (id:4437)
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
- 4437
- isolate
- SB5391
- alias
- 818
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 19 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
- 54
- total length
- 5,334,032 bp
- max length
- 828,918 bp
- mean length
- 98,779 bp
- N50
- 262,838
- L50
- 7
- N90
- 75,132
- L90
- 20
- N95
- 40,714
- L95
- 24
- %GC
- 57.44
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,371
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
- 0
- resistance_score
- 0
- num_resistance_classes
- 5
- num_resistance_genes
- 8
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- unknown (KL45)
- K_type
- unknown (K45)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.83%
- K_locus_missing_genes
- KL45_02_cpsACP,KL45_03_wzi,KL45_04_wza,KL45_05_wzb,KL45_06_wzc,KL45_07_wcaA,KL45_08_wcaJ,KL45_09_wcuP,KL45_10_wclI,KL45_11_wzy,KL45_12_wcqB
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.50%
- AGly_acquired
- aadA2^;strA.v1^;strB.v1
- MLS_acquired
- mphA
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA12
- Bla_chr
- SHV-1^
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 | 121 (39 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 217 (28 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 | 121 (39 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 217 (28 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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