Full information on isolate MVK-04F004 (id:12059)
Projects
This isolate is a member of the following project:
- Rodrigues et al 2022_MSpectrum
- Collection of KpSC genomes studied in 'High prevalence of Klebsiella pneumoniae in EU food as determined using culture and molecular detection methods' (PMID: 35196810)
Provenance/primary metadata
- id
- 12059
- isolate
- MVK-04F004
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 9 updates show details
- date entered
- 2020-02-12
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2019
- country
- France
- continent
- Europe
- host
- environment
- source details
- chicken meat
- source lab
- ANSES
Publication (1)
- Rodrigues C, Hauser K, Cahill N, Ligowska-Marzęta M, Centorotola G, Cornacchia A, Garcia Fierro R, Haenni M, Nielsen EM, Piveteau P, Barbier E, Morris D, Pomilio F, Brisse S (2022). High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods. Microbiol Spectr 10:e0237621
Sequence bin
- contigs
- 54
- total length
- 5,321,953 bp
- max length
- 1,054,705 bp
- mean length
- 98,555 bp
- N50
- 367,543
- L50
- 5
- N90
- 100,699
- L90
- 15
- N95
- 93,106
- L95
- 17
- %GC
- 57.54
- Ns
- 0
- gaps
- 0
- loci tagged
- 696
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
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- KL61
- K_type
- K61
- K_locus_problems
- *
- K_locus_confidence
- Very high
- K_locus_identity
- 96.49%
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- *
- O_locus_confidence
- High
- O_locus_identity
- 94.22%
- Bla_chr
- SHV-1
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_22_32_1_0_0_0_0_0
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 (13481 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 4 (589 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 552 (17 isolates) |
klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13481 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 4 (589 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 552 (17 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2257 (1 isolate) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2522 (1 isolate) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2991 (1 isolate) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3603 (1 isolate) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4120 (1 isolate) |
klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5040 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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