Clostridioides difficile

cellular organismsBacteriaBacillatiBacillotaClostridiaPeptostreptococcalesPeptostreptococcaceaeClostridioides
Synonyms: Clostridium difficile; Peptoclostridium difficile
MCA-BAC-000006
TaxID: 1496 | BacDive: 2582 | Rank: species
Biology & Ecology
Biology
Gram Statusgram-positive
Oxygen Toleranceobligate anaerobe
Morphologybacillus (rod)
Key Traits
  • biofilm-forming
  • spore-forming
  • toxin-producing
Ecology
Primary Nichesgut
Reservoiranimal, environment, human
Transmission
  • fecal-oral
  • healthcare-associated
Metabolites
produces C01468 17847 p-cresol
consumes C00189 16000 ethanolamine · C00270 17012 N-acetylneuraminic acid (sialic acid)
modifies
Clinical Profile
Pathobiont
yes no context dependent unknown
Clinical Rolesopportunistic pathogen; primary pathogen
Typical Specimencolon tissue; stool
Bloom Triggers antibiotic exposure · broad-spectrum beta-lactams · D00277 clindamycin · dietary change · dysbiosis · fluoroquinolones · hospitalization · immunosuppression · inflammation
Risk Contextselderly; ICU / critical care; immunocompromised patients; inflammatory bowel disease (IBD); oncological disease; ongoing antibiotic treatment; post-antibiotic; prior CDI episode; renal insufficiency
AMR Highlights 3004305 multidrug-resistant (MDR)
Virulence Factors VF0592 CbpA · VF0593 CD0873 · VF0598 CD2831 · VF0599 CD3246 · VF0385 CDT · VF0591 Cwp66 · VF0590 Cwp84 · VF0596 CwpV · VF0595 FbpA/Fbp68 · VF0594 GroEL · VF0589 SlpA · VF0376 TcdA · VF0377 TcdB · VF0600 Zmp1
Clinical Associations:
E3
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
Clostridioides difficile is the primary cause of nosocomial gastrointestinal infections in industrialized countries, with incidence, morbidity, and mortality increasing over recent decades.
PMID: 38584858
D003015 Clostridium Infections D003428 Cross Infection H00338 Pseudomembranous colitis
E3
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
Clostridioides difficile causes pseudomembranous colitis and, when left untreated, can progress to toxic megacolon, a potentially life-threatening complication.
PMID: 38584858
D003015 Clostridium Infections D003551 Enterocolitis, Pseudomembranous H00338 Pseudomembranous colitis
E3
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
Clostridioides difficile colonization is highly prevalent in infants, while fewer than 5% of adults are asymptomatic carriers.
PMID: 38584858
D003015 Clostridium Infections
E3
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
Antibiotic-induced disruption of the gut microbiome triggers germination of C. difficile spores into vegetative cells that produce enterotoxins, causing watery diarrhea and colonic inflammation.
PMID: 38584858
D000900 Anti-Bacterial Agents D003015 Clostridium Infections D003967 Diarrhea H00338 Pseudomembranous colitis
E1
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
Clostridioides difficile was identified as the causative pathogen of diarrhea/colitis in one critically ill ICU patient (Patient 43) who had concurrent progressive fecal Enterobacteriaceae enrichment, representing an incidental CDI case within a 51-patient prospective cohort studying ICU-associated gut dysbiosis.
PMID: 36894652
D003428 Cross Infection H00338 Pseudomembranous colitis
E1
E3 — Strong human clinical evidence E2 — Moderate human evidence E1 — Limited / preliminary
In antibiotic-treated mice, cecal cholate levels become elevated while bacterial transformation to secondary bile acids (deoxycholate, lithocholate) is greatly suppressed; this antibiotic-induced shift in the bile acid pool promotes C. difficile spore germination by providing the cholate co-stimulant while removing the inhibitory secondary bile acids that are normally produced by commensal microbiota from primary bile acids.
PMID: 24503131
D001647 Bile Acids and Salts H00338 Pseudomembranous colitis
Last reviewed: 2026-04-03
Evidence Timeline
Related Taxa Shared Niche = same body site   Shared Risk = same vulnerable population