Full information on isolate SB5502 (id:4548)
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
- 4548
- isolate
- SB5502
- alias
- 1229
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 649 updates show details
- date entered
- 2016-11-18
- datestamp
- 2026-02-27
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2016
- 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
- 53
- total length
- 5,175,960 bp
- max length
- 522,288 bp
- mean length
- 97,660 bp
- N50
- 230,593
- L50
- 8
- N90
- 62,561
- L90
- 22
- N95
- 32,290
- L95
- 27
- %GC
- 57.74
- Ns
- 0
- gaps
- 0
- loci tagged
- 724
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 | |
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
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 0
- Bla_chr
- SHV-1^
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Ciprofloxacin_prediction
- wildtype S
- Ciprofloxacin_profile_support
- 90.99% S (N=5168/5680)
- Ciprofloxacin_profile
- 0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 0.25 mg/L [0.25-0.25]
- wzi
- wzi59
- K_locus
- KL3
- K_type
- K3
- K_locus_confidence
- Typeable
- K_locus_problems
- ?2-!
- K_locus_identity
- 99.70%
- K_Missing_expected_genes
- KL3_11;KL3_13_wzx;KL3_10_pglJ;KL3_12
- O_locus
- OL3α/β
- O_type
- O3αβ
- O_locus_confidence
- Untypeable
- O_locus_identity
- 99.15%
- O_Missing_expected_genes
- OL3α/β_04_wzt;OL3α/β_08_wbdC;OL3α/β_06_wbdA;OL3α/β_05_wbdD;OL3α/β_03_wzm;OL3α/β_07_wbdB
Analysis performed: 2026-03-02; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_47_0_7_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL8
- Clonal group
- CG8
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 | 124 (11 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 154 (10 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 | 124 (11 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 154 (10 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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