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Full information on isolate 08-058D (id:2894)

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
2894
isolate
08-058D
sender
Kat Holt, Melbourne U
curator
Auto Tagger
update history
28 updates show details
date entered
2015-06-01
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
2008
country
Vietnam
continent
Asia
source type
Human
host
Human
source details
Sputum
infection
Human_infection
other source info
Respiratory
source lab
Heiman Wertheim
accession number
ERS011802

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
188
total length
5,771,233 bp
max length
441,618 bp
mean length
30,699 bp
N50
173,263
L50
11
N90
33,223
L90
43
N95
20,697
L95
54
%GC
56.89
Ns
18626
gaps
240
loci tagged
3,901

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_S62960896

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
4
resistance_score
1
num_resistance_classes
10
num_resistance_genes
18
Yersiniabactin
ybt 15; ICEKp11 (truncated)
YbST
230-1LV
CbST
0
Aerobactin
iuc 3
AbST
23
SmST
0
RmST
0
wzi
wzi104
K_locus
KL51
K_type
K51
K_locus_confidence
High
K_locus_identity
99.40%
K_locus_missing_genes
KL51_14_wcoZ
O_locus
O1/O2v2
O_type
O2afg
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.45%
AGly_acquired
ant(2'')-Ia;rmtB;strA.v1^;strB.v1
MLS_acquired
mef(B);mphA
Phe_acquired
cmlA1*
Rif_acquired
arr-2
Sul_acquired
sul2;sul3
Tet_acquired
tet(A).v1?;tet(G).v1
Tmt_acquired
dfrA12;dfrA23
Bla_acquired
OXA-10;TEM-1D.v1^
Bla_ESBL_acquired
CTX-M-15;VEB-1
Bla_chr
SHV-1^
Flq_mutations
GyrA-83I;GyrA-87Y;ParC-80I
spurious_resistance_hits
aadA8b?-75%;aadA?-0%;catII.2*?-0%;catII.2*?-0%;floR.v1*?-0%;floR.v2*?-0%;sul1?-0%;sul1?-63%
ybtS
6
ybtX
15
ybtQ
22
ybtP
4
ybtA
1
irp2
356*-0%
irp1
34
ybtU
14
ybtT
1
ybtE
4
fyuA
17
iucA
14
iucB
9
iucC
12
iucD
12
iutA
16

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 (13437 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13416 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental48 (88 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental49 (82 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13437 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13416 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental48 (88 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental49 (82 isolates)

Schemes and loci

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