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Full information on isolate GCA_002848605.1 (id:46780)

Projects

This isolate is a member of the following project:

Hennart_et_al_2022_full_collection
Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230

Provenance/primary metadata

id
46780
isolate
GCA_002848605.1
alias
002SK2
sender
Mélanie Hennart, Institut Pasteur
curator
Auto Tagger
update history
3 updates show details
date entered
2023-03-23
datestamp
2023-03-24
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
isolation year
0
city
Unknown
country
Switzerland
continent
Europe
source type
Unknown
host
Unknown
source details
Unknown
accession number
SAMN08212048

Sequence bin

contigs
3
total length
5,630,984 bp
max length
5,393,461 bp
mean length
1,876,995 bp
N50
5,393,461
L50
1
N90
5,393,461
L90
1
N95
5,393,461
L95
1
%GC
57.20
Ns
0
gaps
0
loci tagged
672

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_S62960696

Analysis

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
0
resistance_score
2
num_resistance_classes
9
num_resistance_genes
14
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi420
K_locus
KL10
K_type
K10
K_locus_problems
-*
K_locus_confidence
High
K_locus_identity
96.74%
K_locus_missing_genes
KL10_06_wzc
O_locus
O3/O3a
O_type
O3/O3a
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
97.98%
AGly_acquired
aac(6')-Ib'.v1;aadA*;aadA*;aph(3')-VI
Flq_acquired
qnrS1
MLS_acquired
ereA2*
Phe_acquired
cmlA5
Rif_acquired
arr-2
Sul_acquired
sul1*
Bla_acquired
OXA-9.v1;TEM-1D.v1^
Bla_ESBL_acquired
CTX-M-15;CTX-M-15
Bla_Carb_acquired
NDM-9
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
Flq_mutations
GyrA-83Y;GyrA-87A;ParC-80I

Analysis performed: 2024-04-17; 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-linkage190experimental50 (740 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental51 (733 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental52 (64 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental54 (64 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental56 (47 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental57 (31 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental58 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental58 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental50 (740 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental51 (733 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental52 (64 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental54 (64 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental56 (47 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental57 (31 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental58 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental58 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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