Home About Us Contact What's New
Home>Organism>Klebsiella PasteurMLST>Isolate information
Help

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
Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
update history
137 updates show details
date entered
2006-09-05
datestamp
2025-07-18
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

method
Sanger
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
6,955

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
Kpn_cgMLST2752272398

Analysis

rMLST species identification

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

Analysis performed: 2025-01-28

Kleborate

species
Klebsiella pneumoniae
species_match
strong
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
virulence_score
0
AGly_acquired
strB.v1;aph(3')-Ia;strA.v1;aadA*;aac(6')-Ib'.v1;ant(2'')-Ia
Phe_acquired
cmlA5;catA1*
Sul_acquired
sul1;sul2
Tet_acquired
tet(D)
Bla_ESBL_acquired
SHV-12
Bla_chr
SHV-11^
SHV_mutations
SHV:p.Leu35Gln;SHV:p.Gly238Ser;SHV:p.Glu240Lys;SHV:p.Leu35Gln
Omp_mutations
OmpK35:p.Gly299fs
Flq_mutations
GyrA:p.Ser83Tyr
truncated_resistance_hits
OXA-9.v1*-42%
resistance_score
1
num_resistance_classes
7
num_resistance_genes
14
Ciprofloxacin_prediction
nonwildtype R
Ciprofloxacin_profile_support
77.67% R (N=80/103)
Ciprofloxacin_profile
1 QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
Ciprofloxacin_MIC_prediction
1 mg/L [1-2]
wzi
wzi50
K_locus
KL52
K_type
K52
K_locus_confidence
Typeable
K_locus_identity
100.00%
O_locus
OL13
O_type
O13
O_locus_confidence
Typeable
O_locus_problems
!
O_locus_identity
96.58%

Analysis performed: 2026-01-15; Kleborate v3.2.4

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_184_0_2_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL38
Clonal group
CG38

Show all thresholds

PrefixThresholdMatching isolates
0_0_184_0_2_078
0_0_184_0_2_0_048
0_0_184_0_2_0_0_024
0_0_184_0_2_0_0_0_012
0_0_184_0_2_0_0_0_0_002
061041312
0_058541312
0_0_18419050
0_0_184_04332
0_0_184_0_2108
0_0_184_0_2_078
0_0_184_0_2_0_048
0_0_184_0_2_0_0_024
0_0_184_0_2_0_0_0_012
0_0_184_0_2_0_0_0_0_002

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-linkage190experimental2 (23 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 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental2 (23 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

Export:
Third party:
Analysis: