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Full information on isolate 03-9138 (id:380)

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
380
isolate
03-9138
aliases
03-9138; SB3332
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history
717 updates show details
date entered
2009-02-10
datestamp
2022-11-03
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2003
country
Martinique
continent
North America
source type
Human
host
Human
source details
Anal pus
infection
Anal abscess
source lab
Institut Pasteur

Publications (3)

  • 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

Sequence bin

contigs
380
total length
5,281,893 bp
max length
103,481 bp
mean length
13,900 bp
N50
27,143
L50
53
N90
7,244
L90
189
N95
4,602
L95
233
%GC
57.08
Ns
3
gaps
2
loci tagged
4,064

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_S62962399

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
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
3
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
YbST
0
CbST
0
Aerobactin
iuc 1
AbST
9
Salmochelin
iro 1
SmST
8
RmpADC
rmp 1; KpVP-1 (truncated)
RmST
38
wzi
wzi157
K_locus
KL2
K_type
K2
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
98.40%
O_locus
O1/O2v2
O_type
O1
O_locus_confidence
High
O_locus_identity
98.96%
O_locus_missing_genes
O1/O2v2_10_gmlA
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
iucA
1
iucB
1
iucC
1
iucD
1
iutA
7
iroB
1
iroC
8
iroD
1
iroN
1
rmpA
2
rmpD
4-0%
rmpC
2
spurious_virulence_hits
rmpA_55*-0%;rmpA_55*-42%

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 schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental102 (26 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental124 (26 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental102 (26 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental124 (26 isolates)

Schemes and loci

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