Full information on isolate cur15505 (id:62)

Projects

This isolate is a member of the following projects:

Public isolates: This project contains the isolates that should be publicly available through the public access database.
published_genomes: All isolates with published genome imported in BIGSdb, and validated for scgMLST_S study
Bialek et al 2014_EID: 167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)

Provenance/primary metadata

id: 62
isolate: cur15505
alias: SB2390
sender: Sylvain Brisse, Institut Pasteur, Paris, France
curator: Auto Tagger
update history: 716 updates show details
date entered: 2006-09-05
datestamp: 2023-01-20
taxonomic designation: K. pneumoniae
phylogroup from ST: Kp1 (7 loci)
QC status: 0000
isolation year: 2002
city: Curacao
country: Curacao
continent: South America
source type: Human
host: Human
source details: Urinary tract
source lab: UMCU (Curacao)
K type: K2
K typing method: C-pattern

Publications (5)

Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
Blin C, Passet V, Touchon M, Rocha EPC, Brisse S (2017). Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 19:1881-1898
Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 43:4178-82
van Westreenen M, Paauw A, Fluit AC, Brisse S, van Dijk W, Verhoef J (2003). Occurrence and spread of SHV extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates in Curacao. J Antimicrob Chemother 52:530-2

Sequence bin

contigs: 11
total length: 5,658,175 bp
max length: 3,152,981 bp
mean length: 514,380 bp
N50: 3,152,981
L50: 1
N90: 350,236
L90: 5
N95: 110,871
L95: 7
%GC: 57.10
Ns: 34919
gaps: 64
loci tagged: 4,179

Show sequence bin

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
Scheme	Scheme loci	Designated loci	Score	Status
MLST	7	7	100
Ribosomal MLST	53	53	100
scgMLST629_S	629	629	100

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
QC_warnings: ambiguous_bases
virulence_score: 1
resistance_score: 0
num_resistance_classes: 3
num_resistance_genes: 7
Yersiniabactin: ybt 10; ICEKp4
YbST: 106
CbST: 0
AbST: 0
SmST: 0
RmST: 0
wzi: wzi2
K_locus: KL2
K_type: K2
K_locus_problems: none
K_locus_confidence: Very high
K_locus_identity: 99.75%
O_locus: O1/O2v1
O_type: O1
O_locus_problems: none
O_locus_confidence: Very high
O_locus_identity: 99.99%
AGly_acquired: aac(6')-Il;aadA1.v1;aadA2^;strA.v1;strB.v1
MLS_acquired: mphA
Tmt_acquired: dfrA12
truncated_resistance_hits: sul1?-0%
ybtS: 3
ybtX: 3
ybtQ: 4
ybtP: 3
ybtA: 3
irp2: 7
irp1: 7
ybtU: 3
ybtT: 3
ybtE: 3
fyuA: 3

Analysis performed: 2023-07-21; 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 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	1 (804 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	81 (146 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	502 (35 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	562 (26 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	665 (12 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	812 (12 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	938 (10 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	1112 (6 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	1 (804 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	81 (146 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	502 (35 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	562 (26 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	665 (12 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	812 (12 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	938 (10 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	1112 (6 isolates)

Schemes and loci

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Tools

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