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Full information on isolate T88 (id:1528)

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)
Rollin et al 2022_IJID
Collection of K. pneumoniae genomes studied in "Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities" (PMID: 34767984)

Provenance/primary metadata

id
1528
isolate
T88
alias
SB4447
sender
Suzanne Bialek, AP-HP
curator
Auto Tagger
update history
724 updates show details
date entered
2013-04-02
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2009
city
Paris
country
France
continent
Europe
source type
Human
host
Human
source details
Cerebrospinal fluid
infection
Meningitis
source lab
D. Decre, Hopital Saint-Antoine, AP-HP

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
  • Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC, Offenstadt G, Maury E, Brisse S, Arlet G (2011). Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France. J Clin Microbiol 49:3012-4
  • Rollin G, Rossi B, Brisse S, Decré D, Leflon-Guibout V, Bert F, Hoffmann I, Decousser JW, Fantin B, Lefort A (2022). Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities. Int J Infect Dis 114:185-191

Sequence bin

contigs
273
total length
5,369,378 bp
max length
188,702 bp
mean length
19,669 bp
N50
41,350
L50
39
N90
10,206
L90
141
N95
6,560
L95
174
%GC
57.24
Ns
2
gaps
1
loci tagged
3,999

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
1
Salmochelin
iro 1
SmST
1
RmpADC
-,rmp 1; KpVP-1 (incomplete),-
RmST
0,28-1LV,0
rmpA2
rmpA2_8-60%
wzi
wzi2
K_locus
KL2
K_type
K2
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.94%
O_locus
O1/O2v1
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.46%
Bla_chr
SHV-1^
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
iroB
1
iroC
1
iroD
1
iroN
1
rmpA
55-60%,15,-
rmpD
-,2,-
rmpC
-,-,2

Analysis performed: 2024-01-29; 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-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1532 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental62 (61 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1532 (2 isolates)

Schemes and loci

Tools

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