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Full information on isolate DU35427_05 (id:3004)

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

Provenance/primary metadata

id
3004
isolate
DU35427_05
sender
Kat Holt, Melbourne U
curator
Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
update history
29 updates show details
date entered
2015-06-01
datestamp
2024-05-03
taxonomic designation
K. quasipneumoniae subsp. similipneumoniae
phylogroup from ST
Kp4 (7 loci)
QC status
0000
isolation year
2005
country
Singapore
continent
Asia
source type
Human
host
Human
source details
Urine
infection
NA
other source info
Environment
source lab
Li Yang Hsu
accession number
ERS011910

Publication (1)

  • Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR (2015). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 112:E3574-81

Sequence bin

contigs
289
total length
5,618,304 bp
max length
343,279 bp
mean length
19,441 bp
N50
127,411
L50
14
N90
23,618
L90
49
N95
8,258
L95
67
%GC
57.57
Ns
7606
gaps
102
loci tagged
3,658

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_S62960696

Analysis

rMLST species identification

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

Analysis performed: 2022-11-02

Kleborate

species
Klebsiella quasipneumoniae subsp. similipneumoniae
species_match
strong
QC_warnings
ambiguous_bases
virulence_score
0
resistance_score
1
num_resistance_classes
7
num_resistance_genes
12
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi233
K_locus
KL1
K_type
K1
K_locus_problems
?-*
K_locus_confidence
Good
K_locus_identity
94.29%
K_locus_missing_genes
KL1_18_manC,KL1_19_manB
O_locus
O5
O_type
O5
O_locus_problems
?-*
O_locus_confidence
Good
O_locus_identity
95.06%
O_locus_missing_genes
O5_01_manC,O5_02_manB
AGly_acquired
aac(6')-Ib-cr.v2;strA.v1^;strB.v1
Flq_acquired
qnrB1.v2^;qnrS1
Sul_acquired
sul2
Tet_acquired
tet(A).v1
Tmt_acquired
dfrA14.v2*
Bla_acquired
LAP-2;OXA-1;TEM-1D.v1^
Bla_ESBL_acquired
CTX-M-15
Bla_chr
OKP-B-2
truncated_resistance_hits
CatB4.v1?-89%

Analysis performed: 2024-02-13; 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-linkage190experimental356 (7 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental938 (4 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental356 (7 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental938 (4 isolates)

Schemes and loci

Tools

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