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Full information on isolate GCA_004179405.1 (id:46784)

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
46784
isolate
GCA_004179405.1
alias
071G9
sender
Mélanie Hennart, Institut Pasteur, France
curator
Auto Tagger
update history
8 updates show details
date entered
2023-03-23
datestamp
2025-07-09
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
isolation year
0
city
Unknown
country
France
continent
Europe
source type
Unknown
host
Unknown
source details
Unknown
accession number
SAMN10840490

Sequence bin

method
Unknown
contigs
313
total length
5,473,720 bp
max length
147,689 bp
mean length
17,488 bp
N50
41,992
L50
39
N90
11,041
L90
131
N95
5,821
L95
165
%GC
57.41
Ns
3741
gaps
52
loci tagged
4,285

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_S62962599
SL147_cgMLST85263174
SL307_cgMLST94788993
Kpn_cgMLST2752269798

Analysis

Kleborate

species
Klebsiella pneumoniae
species_match
strong
QC_warnings
ambiguous_bases
virulence_score
1
resistance_score
2
num_resistance_classes
7
num_resistance_genes
10
Yersiniabactin
ybt 9; ICEKp3
YbST
157-1LV
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi173
K_locus
unknown (KL107)
K_type
unknown (KL107)
K_locus_problems
?-+
K_locus_confidence
None
K_locus_identity
87.85%
K_locus_missing_genes
KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_14,KL107_15
O_locus
unknown (O1/O2v1)
O_type
unknown (O2a)
O_locus_problems
?-
O_locus_confidence
None
O_locus_identity
96.25%
O_locus_missing_genes
O1/O2v1_01_wzm,O1/O2v1_03_wbbM,O1/O2v1_04_glf,O1/O2v1_05_wbbN,O1/O2v1_06_wbbO,O1/O2v1_07_kfoC
AGly_acquired
aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1^;strB.v1
Flq_acquired
qnrB1.v2^
Sul_acquired
sul2
Tmt_acquired
dfrA14.v2*
Bla_acquired
TEM-1D.v1^
Bla_ESBL_acquired
CTX-M-15
Bla_Carb_acquired
OXA-48
Bla_chr
SHV-28.v1^
Omp_mutations
OmpK35-0%
Flq_mutations
GyrA-83I;ParC-80I
truncated_resistance_hits
CatB4.v1?-84%;OXA-1?-0%
ybtS
41
ybtX
11
ybtQ
6
ybtP
25
ybtA
38
irp2
255
irp1
37
ybtU
39
ybtT
5
ybtE
5
fyuA
11

Analysis performed: 2024-04-17; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_369_0_0_0_0_0_1_1
Phylogroup
Kp1
Sublineage
SL307
Clonal group
CG307

Show all thresholds

PrefixThresholdMatching isolates
0_0_369_0_0_071988
0_0_369_0_0_0_041766
0_0_369_0_0_0_0_02805
0_0_369_0_0_0_0_0_11431
0_0_369_0_0_0_0_0_1_1068
061041312
0_058541312
0_0_3691902333
0_0_369_0432330
0_0_369_0_0102262
0_0_369_0_0_071988
0_0_369_0_0_0_041766
0_0_369_0_0_0_0_02805
0_0_369_0_0_0_0_0_11431
0_0_369_0_0_0_0_0_1_1068

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 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental53 (550 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental55 (547 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental56 (310 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental58 (301 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental60 (291 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental61 (177 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental62 (116 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental62 (30 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental53 (550 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental55 (547 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental56 (310 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental58 (301 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental60 (291 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental61 (177 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental62 (116 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental62 (30 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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