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Full information on isolate SB6181 (id:8760)

Projects

This isolate is a member of the following projects:

Barbier et al_ApplEnvironMicrobiol_2020
Collection of KpSC genomes studied in "The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples" (PMID: 32005732)
Isolates Excluded (failed QC)
KlebNET-GSP qc

Provenance/primary metadata

id
8760
isolate
SB6181
alias
MedVetKlebs67
sender
Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
curator
Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history
13 updates show details
date entered
2019-06-05
datestamp
2022-11-30
taxonomic designation
K. pneumoniae
QC status
0002
isolation year
2018
city
Auxonne
country
France
continent
Europe
source type
Environment
host
Environment
source details
soil
other source info
greenhouse beans
source lab
INRA-Dijon
comments
Auxonne

Sequence bin

contigs
150
total length
5,101,581 bp
max length
258,304 bp
mean length
34,011 bp
N50
78,937
L50
19
N90
20,674
L90
68
N95
11,832
L95
84
%GC
58.00
Ns
0
gaps
0
loci tagged
695

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC%GC too high (fail threshold: 57.981)

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962599

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
1
num_resistance_genes
1
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi87
K_locus
unknown (KL50)
K_type
unknown (K50)
K_locus_problems
-*
K_locus_confidence
None
K_locus_identity
90.37%
K_locus_missing_genes
KL50_05_wbaZ,KL50_06_wbaP,KL50_07_wcuU,KL50_08_wcuH,KL50_09_wzx,KL50_10
O_locus
unknown (O3/O3a)
O_type
unknown (O3/O3a)
O_locus_problems
?-+
O_locus_confidence
None
O_locus_identity
90.56%
O_locus_missing_genes
O3/O3a_03_wzm,O3/O3a_04_wzt,O3/O3a_05_wbdD,O3/O3a_06_wbdA
AGly_acquired
aph(3')-IIa
truncated_resistance_hits
LEN-22?-0%;SHV-119*?-0%
spurious_resistance_hits
catA1*?-0%;tet(C)*?-0%

Analysis performed: 2024-03-12; Kleborate v2.3.2

Similar isolates (determined by classification schemes)

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-linkage190experimental131 (65 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental240 (32 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental131 (65 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental240 (32 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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