Full information on isolate BD-DU (id:1521)

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.
Bialek et al 2014_EID: 167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)
Isolates Excluded (failed QC): KlebNET-GSP qc

id: 1521
isolate: BD-DU
alias: SB4565
sender: Suzanne Bialek, AP-HP
curator: Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history: 721 updates show details
date entered: 2013-03-29
datestamp: 2022-11-03
taxonomic designation: K. pneumoniae
phylogroup from ST: Kp1 (7 loci)
QC status: 0100
isolation year: 2011
city: Bordeaux
country: France
continent: Europe
source type: Human
host: Human
source details: Liver pus
infection: Liver abscess
source lab: B. De Barbeyrac, Bordeaux
K type: K1
K typing method: PCR

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

Check	Status	Warn/fail reason
Number of contigs		too many contigs (fail threshold: 501)
Assembly size
Minimum N50		N50 too low (warn threshold: 20,000)
%GC

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	572	90

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Klebsiella pneumoniae	Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae	100%

Analysis performed: 2022-11-02

Database	Best match locus	Best match type	Match confidence	Problems	Identity	Coverage	Length discrepancy	Expected genes in locus	Missing expected genes	Other genes in locus	Other genes in locus, details	Expected genes outside locus	Expected genes outside locus, details	Other genes outside locus	Other genes outside locus, details	Truncated genes, details	Extra genes, details
Klebsiella K locus	KL1	K1	Typeable		99.94%	100.00%	0 bp	20 / 20 (100.00%)		0		0 / 20 (0.00%)		4	KL40_03_wcpO,97.97%,100.00%;KL40_04,99.50%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00%
Klebsiella O locus	OL2α.2	O1αβ,2β	Typeable		99.29%	100.00%	-2 bp	7 / 7 (100.00%)		0		0 / 7 (0.00%)		2	OL3γ_01_manC,99.58%,100.00%;OL3α/β_02_manB,99.78%,97.39%		Extra_genes_wbbYZ_02_wbbY,100.00%,100.00%;Extra_genes_gml2β_03_gmlC,98.56%,100.00%;Extra_genes_gml2β_02_gmlB,99.69%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%;Extra_genes_gml2β_01_gmlA,100.00%,100.00%

Analysis performed: 2025-12-28; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.

species: Klebsiella pneumoniae
species_match: strong
virulence_score: 5
resistance_score: 0
num_resistance_classes: 0
num_resistance_genes: 0
Yersiniabactin: ybt 1; ICEKp10 (incomplete) (truncated)
YbST: 342-4LV
Colibactin: clb 2 (incomplete)
CbST: 27-2LV
Aerobactin: iuc 1 (incomplete)
AbST: 1-2LV
Salmochelin: iro 1 (incomplete)
SmST: 2-1LV
RmpADC: rmp 1; KpVP-1
RmST: 26
rmpA2: rmpA2_5-54%
wzi: wzi1
K_locus: KL1
K_type: K1
K_locus_problems: none
K_locus_confidence: Very high
K_locus_identity: 99.98%
O_locus: O1/O2v2
O_type: O1
O_locus_problems: none
O_locus_confidence: Very high
O_locus_identity: 99.12%
Bla_chr: SHV-11.v1^
SHV_mutations: 35Q
Omp_mutations: OmpK35-82%
ybtS: 2
ybtX: 2*-0%
ybtQ: 8
ybtA: 2
ybtU: 2
ybtT: 2
ybtE: 2
fyuA: 2
clbA: 2
clbB: 2
clbC: 3
clbD: 2
clbE: 2
clbF: 2
clbG: 2
clbH: 3
clbI: 2
clbL: 2
clbM: 2
clbN: 2
clbP: 2
clbQ: 2
iucA: 1
iucC: 1*
iucD: 1
iutA: 1
iroC: 4
iroD: 1
iroN: 1
rmpA: 2
rmpD: 2
rmpC: 2
spurious_virulence_hits: irp2_179*-0%;irp1_245*-0%;irp1_245*-42%;ybtP_2*-0%;irp2_220*-45%;clbO_13*-0%;iucB_1*-0%;iroB_1*-75%

Analysis performed: 2025-10-17; Kleborate v2.3.2

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