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Clostridioides difficile (previously Clostridium difficile) Biological Agent Reference Sheet (BARS)

Updated October 2, 2023
Disclaimer: Risk group, biosafety level, and all other precautions noted here are subject to change after a risk assessment by EHS.


Agent Type Risk Group Biosafety Level Animal Housing Biosafety Level
Bacteria  RG-2 BSL-2 ABSL-2

Agent Characteristics 

Risk Group:  RG-2 associated with human disease, rarely serious; preventive or therapeutic interventions often available.

Agent Type:  Bacteria 

Description: Clostridioides difficile is a Gram positive, anaerobic, rod shaped, spore forming bacteria that causes infectious diarrhea and colitis. Abdominal pain, bloating, and diarrhea are caused by enterotoxin and cytotoxin released by C. difficile. Disease frequently follows antibiotic treatment and normal gut flora disruption, which allows C. difficile to overgrow. The spores of this organism are much more resistant to disinfection. Any surface, device, or material (such as caging, PPE, etc.) that becomes contaminated may serve as a reservoir for C. difficile spores. 

Host Range: Humans, pigs, calves                              Host Shedding: Feces   

Route of Exposure to Humans: Aerosolized droplets that can be swallowed, Direct Contact, Mucous Membranes, Contaminated Items, Ingestion (Primary), Percutaneous, Broken skin

Infectious Dose: Unknown                                

Incubation Period: Most commonly 5-10 days, but can range from 1 day to several weeks

Health Hazards

Signs and symptoms of infection may include:

  • Gastrointestinal symptoms (i.e. loss of appetite, nausea, vomiting, diarrhea)

Immunizations: None available                            Prophylaxis*: Antibiotic treatment available

Antibiotics: Use antibiotics judiciously. Speak with your supervisor or primary healthcare provider before handling Clostridioides difficile culture if you are on antibiotic treatment.

*Formal medical advice is obtained during medical consultations with Cornell Health or primary healthcare provider as needed.

Agent Viability 

Survival Outside Host Disinfection Inactivation

C. difficile is able to survive in soil, meat, and vegetables

1:5 Bleach Dilution 

2% glutaraldehyde, with prolonged contact time; 1:1 dilution of Spor-Klenz Concentrate; Chlorine Dioxide.

Spores are fairly resistant; moderate susceptibility to 1% sodium hypochlorite; susceptible to high level disinfectants (>2% glutaraldehyde) with prolonged contact time.

Special Considerations: 

Because alcohol does not kill Clostridium difficile spores, use of soap and water is more efficacious than alcohol-based hand rubs. However, early experimental data suggest that, even using soap and water, the removal of C. difficile spores is more challenging than the removal or inactivation of other common pathogens.

  • Preventing contamination of the hands via glove use remains the cornerstone for preventing Clostridium difficile transmission. 

For more guidance on disinfection see: disinfectant selection.

Laboratory Hazards 

  • High energy-creating activities (centrifugation, sonication, high pressure systems, vortexing, tube cap popping)

  • Handling of sharps (needles, scalpels, microtome blades, broken glass, etc.)
  • Splash/droplet-creating activities (shaking incubators, liquid culturing, mechanical pipetting)
  • Equipment contamination
  • Exposed skin/uncovered wounds

Laboratory Acquired Infection (LAI) History: none reported. 

Laboratory Handling Guidelines 

Laboratory Biosafety Level (BSL): BSL-2


Lab Engineering Controls Personal Protective Equipment
  • Eye Protection
  • Single gloves
  • Additional gloves
  • Disposable solid front gown
  • Additional mucous membrane protection (where aerosolization is a concern)

Waste Management: Regulated Medical Waste (RMW)

Shipping Guidance: Refer to EHS Biological Materials Shipping 

Animal Vivarium Guidance

Animal Housing Biosafety Level (ABSL): ABSL-2

Animal Biosecurity: Experimental animals are housed separately      

Perform Inoculations: In a Biosafety Cabinet

Change Cages: In a Biosafety Cabinet

Additional Vivarium Guidance: MUST USE: 1:1 Dilution of Spor-Klenz Concentrate for 1 minute of contact time

Exposure and Spill Procedures 

Mucous Membranes: Flush eyes, mouth, or nose for 15 minutes at an eyewash station. See: responding to exposures.

Other Exposures: Wash with soap and water for 15 minutes (open wounds, sores, etc.) or a minimum of 20 seconds for areas with intact skin. See: responding to exposures.

Small Spills: Notify others working in the lab. Evacuate area and allow 30 minutes for aerosols to settle. Don appropriate PPE. Cover area of the spill with paper towels and apply disinfectant, working from the perimeter toward the center. Allow 30 minutes of contact time before disposal and cleanup of spill materials. See: spill cleanup.

Large Spills: Request assistance from the EHS Spill Team by calling CUPD dispatch. Call 911 from a campus phone or 607-255-1111 from a mobile phone.

Incident Reporting: Immediately report the incident to supervisor and complete the EHS online injury/illness report as soon as possible.

Medical Follow-Up:

  • For students, seek medical attention at Cornell Health or local primary care provider. Call Cornell Health at 607-255-5155 (24-hour phone consultation line) or a local urgent care. 

  • For faculty and staff, seek medical evaluation with a local primary care provider or urgent care. Cornell Health does not see employees for post-exposure care. 
  • Emergencies: Call 911 from a campus phone or 607-255-1111 from a mobile phone. 

Cornell EHS would like to thank Emory University for the use of their Biological Agent Reference Sheet (BARS) format and some content. 

More Information


  1. CDC. Clostridioides difficile Infection | HAI | CDC.
  2. Dharmasena M, Jiang X.  Isolation of Toxigenic Clostridium difficile from Animal Manure and Composts Being Used as Biological Soil Amendments. Appl Environ Microbiol. 2018;84(16).
  3. WHO. Guide to appropriate hand hygiene in connection with Clostridium difficile spread - WHO Guidelines on Hand Hygiene in Health Care. Published 2009.