Full information on isolate MVK-05F523 (id:12037)
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
- 12037
- isolate
- MVK-05F523
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Auto Tagger
- update history
- 10 updates show details
- date entered
- 2020-02-12
- datestamp
- 2023-01-21
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2019
- country
- France
- continent
- Europe
- host
- environment
- source details
- salad
- source lab
- AGES
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
- 217
- total length
- 5,644,274 bp
- max length
- 727,887 bp
- mean length
- 26,011 bp
- N50
- 254,644
- L50
- 7
- N90
- 72,316
- L90
- 22
- N95
- 37,837
- L95
- 27
- %GC
- 57.13
- Ns
- 0
- gaps
- 0
- loci tagged
- 698
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
- 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
- KL47
- K_type
- K47
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.19%
- K_locus_missing_genes
- KL47_06_wzc,KL47_12_wcuT
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.51%
- 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_398_1_0_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 | 40 (8 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 | 40 (8 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1262 (1 isolate) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2241 (1 isolate) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2506 (1 isolate) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2973 (1 isolate) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3584 (1 isolate) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4101 (1 isolate) |
klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5021 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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