Strain identifier

BacDive ID: 157670

Type strain: No

Species: Clostridioides difficile

Strain Designation: 3525/15, Goe-91

Strain history: A. E. Zautner, Institut für Medizinische Mikrobiologie. Universitätsmedizin Göttingen; Goe-91

NCBI tax ID(s): 1496 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 8.1 (current version)

General

@ref: 64239

BacDive-ID: 157670

DSM-Number: 105001

keywords: genome sequence, Bacteria, mesophilic, human pathogen

description: Clostridioides difficile 3525/15 is a mesophilic human pathogen that was isolated from Faeces from a symptomatic patient.

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 64239
  • history: A. E. Zautner, Institut für Medizinische Mikrobiologie. Universitätsmedizin Göttingen; Goe-91

doi: 10.13145/bacdive157670.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Clostridioides
  • species: Clostridioides difficile
  • full scientific name: Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

  • synonyms

    @refsynonym
    20215Bacillus difficilis
    20215Peptoclostridium difficile
    20215Clostridium difficile

@ref: 64239

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Clostridioides

species: Clostridioides difficile

full scientific name: Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

strain designation: 3525/15, Goe-91

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64239FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
64239WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

  • @ref: 64239
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose+builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin+builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6838016199urea-hydrolysis
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
64239-++---+--++--++----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
64239------------------+----------
64239------------------+----------
64239-+--------+/--------+----------

Isolation, sampling and environmental information

isolation

  • @ref: 64239
  • sample type: Faeces from a symptomatic patient
  • geographic location: Göttingen
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Infection#Patient

Safety information

risk assessment

  • @ref: 64239
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridioides difficile DSM 105001GCA_014236775completencbi1496
66792Clostridioides difficile strain DSM 1050011496.5450completepatric1496
66792Clostridioides difficile strain FDAARGOS_15281496.6352completepatric1496
66792Clostridioides difficile strain FDAARGOS_15281496.16111completepatric1496
66792Clostridioides difficile strain FDAARGOS_15281496.16089completepatric1496

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno66.221no
gram-positiveyes91.948no
anaerobicyes98.834no
aerobicno97.56no
halophileno94.298no
spore-formingyes95.17no
glucose-utilyes87.538no
thermophileno91.857yes
glucose-fermentyes57.766no
motileyes77.201no

External links

@ref: 64239

culture collection no.: DSM 105001

straininfo link

  • @ref: 110539
  • straininfo: 405378

literature

  • topic: Pathogenicity
  • Pubmed-ID: 30247587
  • title: Characterization of a clinical Clostridioides difficile isolate with markedly reduced fidaxomicin susceptibility and a V1143D mutation in rpoB.
  • authors: Schwanbeck J, Riedel T, Laukien F, Schober I, Oehmig I, Zimmermann O, Overmann J, Gross U, Zautner AE, Bohne W
  • journal: J Antimicrob Chemother
  • DOI: 10.1093/jac/dky375
  • year: 2019
  • mesh: Anti-Bacterial Agents/*pharmacology, Clostridioides difficile/*drug effects/enzymology/genetics/isolation & purification, Clostridium Infections/*microbiology, DNA-Directed RNA Polymerases/*genetics, Fidaxomicin/*pharmacology, Humans, Microbial Sensitivity Tests, *Mutation, Missense, Polymerase Chain Reaction, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64239Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105001Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105001)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
110539Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405378.1