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Full information on isolate NMI3030_19 (id:14504)

Projects

This isolate is a member of the following projects:

Dataset1_ST147_SARA_cours
Dataset containing 25 isolates of ST147 for teaching purposes
Dataset2_CG147_SARA_cours
Dataset containing 59 isolates of CG147 for teaching purposes
Biedrzycka et al 2021_JAC
Collection of K. pneumoniae genomes studied in "Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015–19" (PMID: 34164678)

Provenance/primary metadata

id
14504
isolate
NMI3030_19
sender
Radek Izdebski, National Medecines Institute Chelmska 30/34 00-725 Warsaw, Poland
curator
Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history
17 updates show details
date entered
2020-08-07
datestamp
2026-02-12
taxonomic designation
K. pneumoniae
QC status
0000
isolation year
2019
city
Inowrocław
country
Poland
continent
Europe
source type
Human
host
Human
source details
Unknown

Publication (1)

  • Biedrzycka M, Urbanowicz P, Guzek A, Brisse S, Gniadkowski M, Izdebski R (2021). Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015-19. J Antimicrob Chemother 76:2538-2545

Sequence bin

method
Illumina
contigs
106
total length
5,624,306 bp
max length
606,945 bp
mean length
53,060 bp
N50
340,600
L50
6
N90
68,439
L90
20
N95
39,275
L95
25
%GC
57.07
Ns
0
gaps
0
loci tagged
4,295

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_S62962899
SL147_cgMLST85285199
SL307_cgMLST94765869
Kpn_cgMLST2752274499

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
virulence_score
0
resistance_score
2
num_resistance_classes
9
num_resistance_genes
13
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi64
K_locus
KL64
K_type
K64
K_locus_problems
none
K_locus_confidence
Perfect
K_locus_identity
100.00%
O_locus
O1/O2v1
O_type
O2a
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.64%
AGly_acquired
aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1;strB.v1
Flq_acquired
qnrB1.v1
Phe_acquired
CatB4.v1
Sul_acquired
sul1
Tet_acquired
tet(A).v1
Tmt_acquired
dfrA1.v1
Bla_acquired
OXA-1;TEM-1D.v1^
Bla_ESBL_acquired
CTX-M-15
Bla_Carb_acquired
NDM-1
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
Omp_mutations
OmpK35-7%
Flq_mutations
GyrA-83I;ParC-80I

Analysis performed: 2025-05-14; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_197_0_4_0_2_4_0_0
Phylogroup
Kp1
Sublineage
SL147
Clonal group
CG147

Show all thresholds

PrefixThresholdMatching isolates
0_0_197_0_4_07919
0_0_197_0_4_0_24232
0_0_197_0_4_0_2_4272
0_0_197_0_4_0_2_4_0147
0_0_197_0_4_0_2_4_0_0047
061041312
0_058541312
0_0_1971902451
0_0_197_0432414
0_0_197_0_4101593
0_0_197_0_4_07919
0_0_197_0_4_0_24232
0_0_197_0_4_0_2_4272
0_0_197_0_4_0_2_4_0147
0_0_197_0_4_0_2_4_0_0047

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 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental50 (758 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental51 (750 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental77 (357 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental79 (351 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental82 (179 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental1076 (44 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental1249 (42 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental3707 (25 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental50 (758 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental51 (750 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental77 (357 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental79 (351 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental82 (179 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental1076 (44 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental1249 (42 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental3707 (25 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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