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Full information on isolate SB6428 (id:9490)

Projects

This isolate is a member of the following projects:

Delgado-Blas et al. 2025
Collection of 336 isolates from different ecological sources (soil, WWTP, animals, clinical) recovered from July 2018 to July 2019. Preprint : Pangenome structure and ecological adaptation in the Klebsiella pneumoniae species complex: insights from a geographically and time limited multi-habitat study (doi: https://doi.org/10.64898/2025.12.11.693626)
Barbier et al_ApplEnvironMicrobiol_2020
Collection of KpSC genomes studied in "The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples" (PMID: 32005732)

Provenance/primary metadata

id
9490
isolate
SB6428
alias
MVK-03E066
sender
Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
curator
Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
update history
21 updates show details
date entered
2019-08-08
datestamp
2025-12-05
taxonomic designation
K. pneumoniae
QC status
0000
isolation year
2018
city
Bourgogne-Franche-Comté region
country
France
continent
Europe
source type
Environment
host
Environment
source details
leaves
other source info
Organic vegetable farm-Sample 5 - salad leaves
source lab
INRAE Dijon

Sequence bin

method
Illumina
contigs
57
total length
5,264,142 bp
max length
532,009 bp
mean length
92,354 bp
N50
228,495
L50
9
N90
63,526
L90
25
N95
41,099
L95
30
%GC
57.52
Ns
0
gaps
0
loci tagged
3,453

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_S629629100
Kpn_cgMLST2752274399

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella pneumoniae Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae 100%

Analysis performed: 2022-11-02

Kaptive

Database Best match locusBest match typeMatch confidenceProblemsIdentityCoverageLength discrepancyExpected genes in locusMissing expected genesOther genes in locusOther genes in locus, detailsExpected genes outside locusExpected genes outside locus, detailsOther genes outside locusOther genes outside locus, detailsTruncated genes, detailsExtra genes, details
Klebsiella K locus KL22 K22 Typeable ?2- 99.65% 40.73% n/a 9 / 18 (50.00%) KL22_16_gnd;KL22_15_wcaJ;KL22_08;KL22_14;KL22_11_wzx;KL22_12_rutE;KL22_10_wfeD;KL22_13;KL22_09 0 0 / 18 (0.00%) 2 KL40_05_rfaG,99.18%,96.58%;KL150_19_gmd,100.00%,100.00%
Klebsiella O locus OL2α.1 O1αβ,2α Typeable 98.81% 100.00% -2 bp 7 / 7 (100.00%) 0 0 / 7 (0.00%) 0 Extra_genes_wbbYZ_02_wbbY,100.00%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.63%,100.00%

Klebsiella K locus

2025-12-08T08:04:34.116920 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Klebsiella O locus

2025-12-08T08:04:37.297117 image/svg+xml Matplotlib v3.10.7, https://matplotlib.org/

Analysis performed: 2025-12-08; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.

Kleborate

species
Klebsiella pneumoniae
species_match
strong
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
virulence_score
0
Bla_chr
SHV-33
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
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
wzi37
K_locus
KL22
K_type
K22
K_locus_confidence
Typeable
K_locus_problems
?2-
K_locus_identity
99.65%
K_Missing_expected_genes
KL22_09;KL22_13;KL22_11_wzx;KL22_14;KL22_10_wfeD;KL22_16_gnd;KL22_12_rutE;KL22_15_wcaJ;KL22_08
O_locus
OL2α.1
O_type
O1αβ,2α
O_locus_confidence
Typeable
O_locus_identity
98.81%

Analysis performed: 2025-12-08; Kleborate v3.2.4

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_131_9_0_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL35
Clonal group
CG10386

Show all thresholds

PrefixThresholdMatching isolates
0_0_131_9_0_078
0_0_131_9_0_0_047
0_0_131_9_0_0_0_026
0_0_131_9_0_0_0_0_016
0_0_131_9_0_0_0_0_0_006
061041312
0_058541312
0_0_131190466
0_0_131_9439
0_0_131_9_0109
0_0_131_9_0_078
0_0_131_9_0_0_047
0_0_131_9_0_0_0_026
0_0_131_9_0_0_0_0_016
0_0_131_9_0_0_0_0_0_006

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-linkage190experimental81 (180 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1315 (8 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental81 (180 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1315 (8 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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