Full information on isolate SB4814 (id:1796)

Projects

This isolate is a member of the following project:

Isolates Excluded (failed QC): KlebNET-GSP qc

Provenance/primary metadata

id: 1796
isolate: SB4814
alias: IPEUC1042
sender: Jonathan Cotrupi, Institut Pasteur
curator: Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history: 19 updates show details
embargo history: show details
date entered: 2014-07-31
datestamp: 2025-07-18
taxonomic designation: K. pneumoniae
phylogroup from ST: Kp1 (7 loci)
QC status: 0020
isolation year: 1985
city: Le Pin
country: France
continent: Europe
host: horse
source details: genital tract
source lab: LDRBH (Caen)
K type: 1
K typing method: Antiserum

Sequence bin

method: Illumina
contigs: 193
total length: 16,500,442 bp
max length: 1,291,645 bp
mean length: 85,495 bp
N50: 275,229
L50: 16
N90: 43,761
L90: 62
N95: 29,955
L95: 85
%GC: 57.31
Ns: 0
gaps: 0
loci tagged: 2,552

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size		assembly size too large (fail threshold: 6,132,847)
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

Kaptive

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	?3	99.97%	300.00%	n/a	20 / 20 (100.00%)		0		0 / 20 (0.00%)		12	KL40_03_wcpO,97.97%,100.00%;KL40_03_wcpO,97.97%,100.00%;KL40_03_wcpO,97.97%,100.00%;KL40_04,99.50%,100.00%;KL40_04,99.50%,100.00%;KL40_04,99.50%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL40_05_rfaG,99.74%,100.00%;KL150_19_gmd,99.10%,100.00%;KL150_19_gmd,99.10%,100.00%;KL150_19_gmd,99.10%,100.00%
Klebsiella O locus	OL2α.2	O1αβ,2β	Typeable	?3	99.29%	300.00%	n/a	7 / 7 (100.00%)		0		0 / 7 (0.00%)		6	OL3γ_01_manC,99.58%,100.00%;OL3γ_01_manC,99.58%,100.00%;OL3γ_01_manC,99.58%,100.00%;OL3α/β_02_manB,99.78%,97.39%;OL3α/β_02_manB,99.78%,97.39%;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%

Klebsiella K locus

Klebsiella O locus

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

Kleborate

species: Klebsiella pneumoniae
species_match: strong
QC_warnings: total_size
YbST: 47,ST47,ST47
Yersiniabactin: ybt 1; ICEKp10,ybt 1; ICEKp10,ybt 1; ICEKp10
ybtS: 2,2,2
ybtX: 2,2,2
ybtQ: 2,2,2
ybtP: 2,2,2
ybtA: 2,2,2
irp2: 6,6,6
irp1: 6,6,6
ybtU: 2,2,2
ybtT: 2,2,2
ybtE: 2,2,2
fyuA: 2,2,2
CbST: 29
Colibactin: clb 2
clbA: 2
clbB: 2
clbC: 2
clbD: 2
clbE: 2
clbF: 2
clbG: 2
clbH: 3
clbI: 2
clbL: 2
clbM: 2
clbN: 2
clbO: 2
clbP: 2
clbQ: 2
AbST: 1,ST1,ST1
Aerobactin: iuc 1,iuc 1,iuc 1
iucA: 1,1,1
iucB: 1,1,1
iucC: 1,1,1
iucD: 1,1,1
iutA: 1,1,1
SmST: 2-2LV
Salmochelin: iro 1 (incomplete)
iroB: 1
iroC: 4
RmST: 0
rmpA: 40*-60%
virulence_score: 5
rmpA2: rmpA2_6-60%,rmpA2_6-60%,rmpA2_6-60%
AGly_acquired: aadA^;aadA^;aadA^;aph3-Ia.v1^;aph3-Ia.v1^;aph3-Ia.v1^
Sul_acquired: sul1;sul1;sul1
Tet_acquired: tet(C);tet(C);tet(C)
Bla_chr: SHV-11^;SHV-11^;SHV-11^
SHV_mutations: SHV:p.Leu35Gln;SHV:p.Leu35Gln;SHV:p.Leu35Gln
resistance_score: 0
num_resistance_classes: 3
num_resistance_genes: 12
Ciprofloxacin_prediction: wildtype S
Ciprofloxacin_profile_support: 90.99% S (N=5168/5680)
Ciprofloxacin_profile: 0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
Ciprofloxacin_MIC_prediction: 0.25 mg/L [0.25-0.25]
wzi: wzi1
K_locus: KL1
K_type: K1
K_locus_confidence: Typeable
K_locus_problems: ?3
K_locus_identity: 99.97%
O_locus: OL2Î±.2
O_type: O1Î±Î²,2Î²
O_locus_confidence: Typeable
O_locus_problems: ?3
O_locus_identity: 99.29%

Analysis performed: 2025-12-28; Kleborate v3.2.4

Similar isolates (determined by LIN codes)

Scheme: scgMLST629_S
LIN code: 0_0_429_0_44_1_1_0_3_0
Phylogroup: Kp1
Sublineage: SL23
Clonal group: CG23

Show all thresholds Hide larger thresholds

Prefix	Threshold	Matching isolates
0_0_429_0_44_1	7	19
0_0_429_0_44_1_1	4	11
0_0_429_0_44_1_1_0	2	9
0_0_429_0_44_1_1_0_3	1	2
0_0_429_0_44_1_1_0_3_0	0	2
0	610	41312
0_0	585	41312
0_0_429	190	492
0_0_429_0	43	490
0_0_429_0_44	10	49
0_0_429_0_44_1	7	19
0_0_429_0_44_1_1	4	11
0_0_429_0_44_1_1_0	2	9
0_0_429_0_44_1_1_0_3	1	2
0_0_429_0_44_1_1_0_3_0	0	2

Schemes and loci

All loci

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