Strain identifier
BacDive ID: 23854
Type strain:
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)
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/bacdive23854.20230509.8.1
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
@ref synonym 20215 Bacillus difficilis 20215 Peptoclostridium difficile 20215 Clostridium 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
@ref | cell shape | gram stain | confidence |
---|---|---|---|
68367 | rod-shaped | ||
68367 | positive | ||
69480 | positive | 100 |
colony morphology
- @ref: 20943
- type of hemolysis: gamma
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
20943 | WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) | yes | https://mediadive.dsmz.de/medium/339 | Name: 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 |
20943 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: 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 |
20943 | FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) | yes | https://mediadive.dsmz.de/medium/1203 | Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20943 | positive | growth | 37 | mesophilic |
53868 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
20943 | anaerobe | |
53868 | anaerobe | |
69480 | anaerobe | 99.593 |
spore formation
@ref | spore formation | confidence |
---|---|---|
68367 | yes | |
69481 | yes | 98 |
69480 | yes | 99.714 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | - | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | - | builds acid from |
68367 | 17057 | cellobiose | - | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 65327 | D-xylose | - | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | - | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | - | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | - | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
20943 | catalase | + | 1.11.1.6 |
20943 | cytochrome-c oxidase | - | 1.9.3.1 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | catalase | + | 1.11.1.6 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | CAT | SPOR | GRAM | COCC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20943 | - | - | + | + | - | - | - | - | - | - | + | + | - | - | + | + | - | - | - | - | ||||
20943 | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | + | + | + | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridioides difficile 1470 | GCA_900243225 | scaffold | ncbi | 1496 |
66792 | Clostridioides difficile ATCC 43598 | GCA_008868185 | contig | ncbi | 1496 |
66792 | Clostridioides difficile strain ATCC 43598 | 1496.4858 | wgs | patric | 1496 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 98 | no |
flagellated | no | 67.022 | no |
gram-positive | yes | 92.445 | no |
anaerobic | yes | 98.763 | no |
aerobic | no | 97.023 | yes |
halophile | no | 92.518 | no |
spore-forming | yes | 94.374 | yes |
thermophile | no | 91.786 | no |
glucose-util | yes | 89.031 | no |
motile | yes | 77.785 | no |
glucose-ferment | yes | 57.822 | no |
External links
@ref: 20943
culture collection no.: DSM 27544, ATCC 43598, NCTC 13569, CCUG 37782
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Enzymology | 21391503 | In 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 LC | J AOAC Int | 2011 | Clostridioides 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 Agency | Phylogeny | |
Pathogenicity | 25241189 | Evaluation 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 NY | Diagn Microbiol Infect Dis | 2014 | Bacterial 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 Specificity | Enzymology | 10.1016/j.diagmicrobio.2014.08.014 |
Pathogenicity | 33148316 | Disinfectant wipes transfer Clostridioides difficile spores from contaminated surfaces to uncontaminated surfaces during the disinfection process. | Nkemngong CA, Chaggar GK, Li X, Teska PJ, Oliver HF | Antimicrob Resist Infect Control | 2020 | Clostridioides difficile/*drug effects, Disinfectants/*pharmacology, Disinfection/*methods, Hydrogen Peroxide/pharmacology, Spores, Bacterial/*drug effects | 10.1186/s13756-020-00844-0 |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
20943 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27544 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27544) | |
53868 | Curators of the CCUG | https://www.ccug.se/strain?id=37782 | Culture Collection University of Gothenburg (CCUG) (CCUG 37782) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68367 | Automatically annotated from API 20A | |||
68380 | Automatically annotated from API rID32A | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |