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Clostridioides difficile (Prevot) Lawson et al.


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Clostridioides difficile strain 90556-M6S [L.S. McClung 1780] is a whole-genome sequenced bacterial type strain with applications in enteric and infectious disease research. This strain is confirmed to have the tcdA and tcdB genes.
Product category
Product type
Strain designation
90556-M6S [L.S. McClung 1780]
Type strain
Genome sequenced strain
Enteric disease research
Infectious disease research
Product format
Storage conditions
2°C to 8°C
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ATCC determines the biosafety level of a material based on our risk assessment as guided by the current edition of Biosafety in Microbiological and Biomedical Laboratories (BMBL), U.S. Department of Health and Human Services. It is your responsibility to understand the hazards associated with the material per your organization’s policies and procedures as well as any other applicable regulations as enforced by your local or national agencies.

ATCC highly recommends that appropriate personal protective equipment is always used when handling vials. For cultures that require storage in liquid nitrogen, it is important to note that some vials may leak when submersed in liquid nitrogen and will slowly fill with liquid nitrogen. Upon thawing, the conversion of the liquid nitrogen back to its gas phase may result in the vial exploding or blowing off its cap with dangerous force creating flying debris. Unless necessary, ATCC recommends that these cultures be stored in the vapor phase of liquid nitrogen rather than submersed in liquid nitrogen.

Detailed product information


Specific applications
Produces cytotoxin
Enteric Research


Toxinotype: 0
Toxin genes
cdtB (Binary toxin) negative
tcdA (Toxin A) positive
tcdB (Toxin B) positive
Presence of tcdA and tcdB genes confirmed by PCR. RefLemee L, et al. Multiplex PCR targeting tpi (triose phosphate isomerase), tcdA (Toxin A), and tcdB (Toxin B) genes for toxigenic culture of Clostridium difficile. J. Clin. Microbiol. 42(12): 5710-5714, 2004. PubMed: 15583303
Binary toxin gene cdtB not amplified by PCR
Toxinotype 0
Ribotype 001

Handling information

Handling procedure
  1. Open vial.
  2. Under anaerobic conditions aseptically rehydrate the entire pellet with approximately 0.5 mL of #2107 broth. Aseptically transfer the entire contents to a 5-6 mL tube of #2107 broth. Additional test tubes can be inoculated by transferring 0.5 mL of the primary broth tube to these secondary broth tubes. Best practice dictates the use of pre-reduced media.
  3. Use several drops of the primary broth tube to inoculate a #260 plate.
  4. Incubate in an anaerobic atmosphere at 37°C for 48 hours. Incubate one agar plate aerobically at 37°C to check for contamination.

Anaerobic conditions for transfer may be obtained by the use of an anaerobic gas chamber or placement of test tubes under a gassing cannula system connected to anaerobic gas.

Anaerobic conditions for incubation may be obtained by any of the following:

  • Loose screw caps on test tubes in an anaerobic chamber
  • Loose screw caps on test tubes in an activated anaerobic gas pack jar
  • Use of sterile butyl rubber stoppers on test tubes so that an anaerobic gas headspace is retained
Handling notes
Anaerobe Systems Brucella Blood Plate (AS-111 or AS-141) can be used to analyze colony morphology and purity.
The presence of tcdA and tcdB genes is confirmed by PCR. The binary toxin gene cdtB is not amplified by PCR.
Purified genomic DNA of this strain is available (ATCC 9689D-5).
Additional information on this culture is available on the ATCC web site at

Quality control specifications

Verification method
Whole-genome Sequencing


Deposited as
Clostridium difficile (Hall and O'Toole) Prevot
FE Clark
Chain of custody
ATCC <-- F E Clark
Special collection
NSF - Bacteriology
Cross references
GenBank X94328 C.difficile spo0A gene.
GenBank AX110003 Sequence 736 from Patent WO0123604.
GenBank AX110007 Sequence 740 from Patent WO0123604.
GenBank AX110095 Sequence 828 from Patent WO0123604.
GenBank AX111484 Sequence 2217 from Patent WO0123604.
GenBank AX111505 Sequence 2238 from Patent WO0123604.
GenBank AX111525 Sequence 2258 from Patent WO0123604.
GenBank U36481 Clostridium difficile sporulation protein homolog (spo0A) gene, partial cds.
GenBank S51968 {16S/23S ribosomal DNA spacer region} [Clostridium difficile, ATCC 9689, Genomic, 271 nt]
GenBank U43514 Clostridium difficile putative spoIVB (spoIVB) gene, complete cds, and phosphorylation-activated transcription factor spo0A (spo0a) gene, complete cds.

Legal disclaimers

Intended use
This product is intended for laboratory research use only. It is not intended for any animal or human therapeutic use, any human or animal consumption, or any diagnostic use.

The product is provided 'AS IS' and the viability of ATCC® products is warranted for 30 days from the date of shipment, provided that the customer has stored and handled the product according to the information included on the product information sheet, website, and Certificate of Analysis. For living cultures, ATCC lists the media formulation and reagents that have been found to be effective for the product. While other unspecified media and reagents may also produce satisfactory results, a change in the ATCC and/or depositor-recommended protocols may affect the recovery, growth, and/or function of the product. If an alternative medium formulation or reagent is used, the ATCC warranty for viability is no longer valid.  Except as expressly set forth herein, no other warranties of any kind are provided, express or implied, including, but not limited to, any implied warranties of merchantability, fitness for a particular purpose, manufacture according to cGMP standards, typicality, safety, accuracy, and/or noninfringement.


This product is intended for laboratory research use only. It is not intended for any animal or human therapeutic use, any human or animal consumption, or any diagnostic use. Any proposed commercial use is prohibited without a license from ATCC.

While ATCC uses reasonable efforts to include accurate and up-to-date information on this product sheet, ATCC makes no warranties or representations as to its accuracy. Citations from scientific literature and patents are provided for informational purposes only. ATCC does not warrant that such information has been confirmed to be accurate or complete and the customer bears the sole responsibility of confirming the accuracy and completeness of any such information.

This product is sent on the condition that the customer is responsible for and assumes all risk and responsibility in connection with the receipt, handling, storage, disposal, and use of the ATCC product including without limitation taking all appropriate safety and handling precautions to minimize health or environmental risk. As a condition of receiving the material, the customer agrees that any activity undertaken with the ATCC product and any progeny or modifications will be conducted in compliance with all applicable laws, regulations, and guidelines. This product is provided 'AS IS' with no representations or warranties whatsoever except as expressly set forth herein and in no event shall ATCC, its parents, subsidiaries, directors, officers, agents, employees, assigns, successors, and affiliates be liable for indirect, special, incidental, or consequential damages of any kind in connection with or arising out of the customer's use of the product. While reasonable effort is made to ensure authenticity and reliability of materials on deposit, ATCC is not liable for damages arising from the misidentification or misrepresentation of such materials.

Please see the material transfer agreement (MTA) for further details regarding the use of this product. The MTA is available at

Permits & Restrictions

Import Permit for the State of Hawaii

If shipping to the U.S. state of Hawaii, you must provide either an import permit or documentation stating that an import permit is not required. We cannot ship this item until we receive this documentation. Contact the Hawaii Department of Agriculture (HDOA), Plant Industry Division, Plant Quarantine Branch to determine if an import permit is required.



Curated Citations

Rolfe RD, Finegold SM. Purification and characterization of Clostridium difficile toxin. Infect. Immun. 25: 191-201, 1979. PubMed: 478634

Florin I, Thelestam M. Intoxication of cultured human lung fibroblasts with Clostridium difficile toxin. Infect. Immun. 33: 67-74, 1981. PubMed: 6167521

Skerman VB, et al. Approved lists of bacterial names. Int J Syst Bacteriol 30: 225-420, 1980.

Rupnik, M et al. A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates. J. Clin. Microbiol. 36(8): 2240-2247, 1998. PubMed: 9665999

Fawley WN, Wilcox MH; on behalf of the Clostridium difficile Ribotyping Network for England and N. Ireland (CDRN). An enhanced DNA fingerprinting service to investigate potential Clostridium difficile infection case clusters sharing the same PCR-ribotype. J. Clin. Microbiol. 49(12): 4333-4337, 2011. PubMed: 21956986

View All Curated Citations for this Product

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