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Full information on isolate CDC4241-71 (id:1556)

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
Hennart et al. 2022_MBE
Reference Genomes for LINcodes (Table S9) (PMID: 35700230)

Provenance/primary metadata

id
1556
isolate
CDC4241-71
aliases
CDC 4241-71; SB94
sender
Suzanne Bialek, AP-HP
curator
Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history
1328 updates show details
date entered
2013-04-11
datestamp
2023-01-13
taxonomic designation
K. variicola subsp. tropica
phylogroup from ST
Kp5 (7 loci)
QC status
0000
country
Unknown
source type
Environment
host
Environment
source details
Unknown
source lab
Institut Pasteur, BBPE
comments
Kp5 type alleles

Publications (2)

  • 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
  • Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:

Sequence bin

contigs
57
total length
5,495,631 bp
max length
521,438 bp
mean length
96,415 bp
N50
160,754
L50
10
N90
53,265
L90
31
N95
37,525
L95
37
%GC
57.19
Ns
1
gaps
1
loci tagged
3,713

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_S62961297

Analysis

rMLST species identification

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

Analysis performed: 2022-12-01

Kleborate

species
Klebsiella variicola subsp. tropica
species_match
strong
QC_warnings
ambiguous_bases
virulence_score
0
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi166
K_locus
KL23
K_type
K23
K_locus_problems
?-*
K_locus_confidence
Good
K_locus_identity
87.87%
K_locus_missing_genes
KL23_09_wckU
O_locus
OL103
O_type
unknown (OL103)
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.24%
Bla_chr
LEN-38

Analysis performed: 2024-01-29; Kleborate v2.3.2

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental6 (21 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental6 (21 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental16 (1 isolate)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental16 (1 isolate)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental16 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental16 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental16 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental16 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental16 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental16 (1 isolate)

Schemes and loci

Tools

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