Full information on isolate SB5578 (id:4624)
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
- 4624
- isolate
- SB5578
- alias
- 1321
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 653 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
- 83
- total length
- 5,302,597 bp
- max length
- 361,106 bp
- mean length
- 63,887 bp
- N50
- 141,350
- L50
- 12
- N90
- 37,658
- L90
- 39
- N95
- 24,498
- L95
- 48
- %GC
- 57.58
- Ns
- 0
- gaps
- 0
- loci tagged
- 749
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 | 625 | 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
- 20
- Aerobactin
- iuc 1
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 3
- SmST
- 14
- Salmochelin
- iro 1
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 3
- RmST
- 57-2LV
- RmpADC
- rmp 1; KpVP-1 (incomplete) (truncated)
- rmpA
- 38*-47%
- rmpC
- 2
- spurious_rmst_hits
- rmpA_40*-47%
- virulence_score
- 3
- spurious_virulence_hits
- rmpA_40*47%
- 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
- wzi72
- K_locus
- KL2
- K_type
- K2
- K_locus_confidence
- Typeable
- K_locus_problems
- ?2-
- K_locus_identity
- 99.46%
- K_Missing_expected_genes
- KL2_12;KL2_09;KL2_07;KL2_13;KL2_08;KL2_11_wzx;KL2_10
- O_locus
- OL3α/β
- O_type
- O3αβ
- O_locus_confidence
- Untypeable
- O_locus_identity
- 99.68%
- O_Missing_expected_genes
- OL3α/β_05_wbdD;OL3α/β_04_wzt;OL3α/β_07_wbdB;OL3α/β_06_wbdA;OL3α/β_03_wzm;OL3α/β_08_wbdC
Analysis performed: 2026-03-02; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_390_0_2_1_1_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL375
- Clonal group
- CG375
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 | 41 (25 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (25 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 | 41 (25 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 41 (25 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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