Full information on isolate MVK-05F569 (id:12045)
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
- 12045
- isolate
- MVK-05F569
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 12 updates show details
- date entered
- 2020-02-12
- datestamp
- 2024-05-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2019
- country
- Austria
- continent
- Europe
- host
- environment
- source details
- chicken meat
- 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
- 189
- total length
- 5,292,096 bp
- max length
- 779,357 bp
- mean length
- 28,001 bp
- N50
- 313,551
- L50
- 6
- N90
- 86,693
- L90
- 20
- N95
- 34,846
- L95
- 24
- %GC
- 57.55
- Ns
- 0
- gaps
- 0
- loci tagged
- 710
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 | 626 | 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
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 26; ICEKp18
- YbST
- 160-1LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi447
- K_locus
- unknown (KL124)
- K_type
- unknown (KL124)
- K_locus_problems
- ?-
- K_locus_confidence
- Low
- K_locus_identity
- 95.07%
- K_locus_missing_genes
- KL124_17_wclK,KL124_19_rmlA,KL124_20_rmlD
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 92.20%
- O_locus_missing_genes
- OL101_02_rfbA,OL101_03_rfbD,OL101_09_glycosylhydrolase
- Bla_chr
- SHV-1
- spurious_resistance_hits
- fosA7*?-0%
- ybtS
- 44
- ybtX
- 61
- ybtQ
- 58
- ybtP
- 65
- ybtA
- 40
- irp2
- 242
- irp1
- 140
- ybtU
- 45
- ybtT
- 38
- ybtE
- 63
- fyuA
- 66
Analysis performed: 2024-03-12; Kleborate v2.3.2
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 (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 | 772 (6 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1267 (5 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 | 772 (6 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1267 (5 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2248 (1 isolate) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2513 (1 isolate) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2980 (1 isolate) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3591 (1 isolate) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4108 (1 isolate) |
klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5028 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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