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Full information on isolate MVK-06F117 (id:12008)

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
12008
isolate
MVK-06F117
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
Denmark
continent
Europe
host
environment
source details
chicken meat
source lab
SSI

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
148
total length
5,123,487 bp
max length
230,930 bp
mean length
34,619 bp
N50
78,515
L50
24
N90
24,031
L90
70
N95
13,831
L95
84
%GC
57.83
Ns
0
gaps
0
loci tagged
714

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962499

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
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
unknown (KL5)
K_type
unknown (K5)
K_locus_problems
?-+*
K_locus_confidence
None
K_locus_identity
86.34%
K_locus_missing_genes
KL5_05_wzb,KL5_06_wzc,KL5_07,KL5_08_wzx,KL5_09,KL5_10,KL5_11,KL5_12,KL5_13,KL5_14,KL5_15_wcaJ,KL5_17_manC,KL5_18_manB
O_locus
O3/O3a
O_type
O3/O3a
O_locus_problems
?-*
O_locus_confidence
Good
O_locus_identity
95.42%
O_locus_missing_genes
O3/O3a_01_manC,O3/O3a_02_manB
Bla_chr
SHV-1^

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 schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental204 (5 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1250 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental204 (5 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1250 (2 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental2221 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental2485 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental2949 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental3559 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental4076 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental4995 (1 isolate)

Schemes and loci

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Tools

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