Strain identifier

BacDive ID: 23854

Type strain: No

Species: Clostridioides difficile

Strain Designation: 1470

Strain history: <- P. Bracegirdle, Health Protection Agency Culture Collections, Salisbury, United Kingdom; NCTC 13569

NCBI tax ID(s): 1496 (species)

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General

@ref: 20943

BacDive-ID: 23854

DSM-Number: 27544

keywords: genome sequence, Bacteria, anaerobe, spore-forming, mesophilic, rod-shaped, human pathogen

description: Clostridioides difficile 1470 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from Faeces, Human .

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 20943
  • history: <- P. Bracegirdle, Health Protection Agency Culture Collections, Salisbury, United Kingdom; NCTC 13569

doi: 10.13145/bacdive23854.20250331.9.3

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
    20215Peptoclostridium difficile
    20215Bacillus difficilis
    20215Clostridium difficile

@ref: 20943

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: 1470

type strain: no

Morphology

cell morphology

@refcell shapegram stain
68367rod-shaped
68367positive

colony morphology

  • @ref: 20943
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20943WILKINS-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
20943CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
20943FASTIDIOUS 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

culture temp

@refgrowthtypetemperature
20943positivegrowth37
53868positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20943anaerobe
53868anaerobe
125439facultative anaerobe96

spore formation

  • @ref: 68367
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838016634raffinose-fermentation
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016199urea-hydrolysis
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+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
6836716199urea-hydrolysis
6836727897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6836735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
20943catalase+1.11.1.6
20943cytochrome-c oxidase-1.9.3.1
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380leucine arylamidase+3.4.11.1
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380L-arginine arylamidase-
68380alpha-fucosidase-3.2.1.51
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367catalase+1.11.1.6
68367beta-glucosidase+3.2.1.21
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
20943--++------++--++----
20943-----------+--------+++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20943------------------+-+/-+-+/------

Isolation, sampling and environmental information

isolation

  • @ref: 20943
  • sample type: Faeces, Human (faeces of asymptomatic neonate)
  • country: Belgium
  • origin.country: BEL
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 20943
  • 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 1470GCA_900243225scaffoldncbi1496
66792Clostridioides difficile ATCC 43598GCA_008868185contigncbi1496
66792Clostridioides difficile strain ATCC 435981496.4858wgspatric1496

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes58.24no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.334no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.211yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes67.152yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.04yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.653no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes74.5
125439BacteriaNetmotilityAbility to perform movementyes78.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive83.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe96

External links

@ref: 20943

culture collection no.: DSM 27544, ATCC 43598, NCTC 13569, CCUG 37782

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology21391503In vitro production of Clostridium difficile spores for use in the efficacy evaluation of disinfectants: a precollaborative investigation.Hasan JA, Japal KM, Christensen ER, Samalot-Freire LCJ AOAC Int2011Clostridioides difficile/*drug effects/isolation & purification/physiology, Disinfectants/*pharmacology, Environmental Microbiology, Microbial Sensitivity Tests, Microbiological Techniques, Spores, Bacterial/*drug effects/isolation & purification, United States, United States Environmental Protection AgencyPhylogeny
Pathogenicity25241189Evaluation of the illumigene C. difficile assay for toxigenic Clostridium difficile detection: a prospective study of 302 consecutive clinical fecal samples.Hong G, Park KS, Ki CS, Lee NYDiagn Microbiol Infect Dis2014Bacterial Toxins/*analysis/genetics, Clostridioides difficile/genetics/*isolation & purification, Clostridium Infections/*diagnosis/microbiology, Diarrhea/*diagnosis/microbiology, Enterotoxins/*analysis/genetics, Feces/*microbiology, Humans, Immunoassay/methods, Nucleic Acid Amplification Techniques/*methods, Predictive Value of Tests, Prospective Studies, Sensitivity and SpecificityEnzymology10.1016/j.diagmicrobio.2014.08.014
Pathogenicity33148316Disinfectant wipes transfer Clostridioides difficile spores from contaminated surfaces to uncontaminated surfaces during the disinfection process.Nkemngong CA, Chaggar GK, Li X, Teska PJ, Oliver HFAntimicrob Resist Infect Control2020Clostridioides difficile/*drug effects, Disinfectants/*pharmacology, Disinfection/*methods, Hydrogen Peroxide/pharmacology, Spores, Bacterial/*drug effects10.1186/s13756-020-00844-0

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
20943Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27544Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27544)
53868Curators of the CCUGhttps://www.ccug.se/strain?id=37782Culture Collection University of Gothenburg (CCUG) (CCUG 37782)
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG