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Full information on isolate MGH 78578 (id:25)

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)
Hennart et al. 2022_MBE
Reference Genomes for LINcodes (Table S9) (PMID: 35700230)

Provenance/primary metadata

id
25
isolate
MGH 78578
aliases
ATCC 700721; SB107
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history
129 updates show details
date entered
2006-09-05
datestamp
2022-11-03
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
isolation year
1994
country
Unknown
source type
Human
host
Human
source details
Blood
infection
Pneumonia
source lab
UMCU (Utrecht, NL)
K type
K52
duplicate number
1
comments
Plasmid accession numbers are NC_009649, NC_009650, NC_009651, NC_009652, NC_009653
accession number
NC_009648, NC_009649, NC_009650, NC_009651

Publications (7)

  • 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
  • Brisse S, Passet V, Grimont PAD (2014). Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol 64:3146-3152
  • Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 43:4178-82
  • Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
  • Ogawa W, Li DW, Yu P, Begum A, Mizushima T, Kuroda T, Tsuchiya T (2005). Multidrug resistance in Klebsiella pneumoniae MGH78578 and cloning of genes responsible for the resistance. Biol Pharm Bull 28:1505-8

Sequence bin

contigs
6
total length
5,694,894 bp
max length
5,315,120 bp
mean length
949,149 bp
N50
5,315,120
L50
1
N90
5,315,120
L90
1
N95
175,879
L95
2
%GC
57.15
Ns
0
gaps
0
loci tagged
4,235

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_S62962799

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella pneumoniae Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae 100%

Analysis performed: 2024-02-03

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
0
resistance_score
1
num_resistance_classes
7
num_resistance_genes
14
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi50
K_locus
KL52
K_type
K52
K_locus_problems
none
K_locus_confidence
Perfect
K_locus_identity
100.00%
O_locus
OL101
O_type
unknown (OL101)
O_locus_problems
*
O_locus_confidence
High
O_locus_identity
94.91%
AGly_acquired
aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1
Phe_acquired
catA1*;cmlA5
Sul_acquired
sul1;sul2
Tet_acquired
tet(D)
Bla_acquired
TEM-1D.v1^;TEM-1D.v1^
Bla_ESBL_acquired
SHV-12
Bla_chr
SHV-11.v1^
SHV_mutations
238S;240K;35Q;35Q
Omp_mutations
OmpK35-86%
Flq_mutations
GyrA-83Y
truncated_resistance_hits
OXA-9.v1*-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-linkage190experimental2 (19 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental2 (8 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental2 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental2 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental2 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental2 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental2 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental2 (19 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental2 (8 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental2 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental2 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental2 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental2 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental2 (2 isolates)

Schemes and loci

Tools

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