Clostridioides difficile

Testing Indications

Note to Submitters

C. difficile testing will not be performed on children less than 12 months old, as this group has been shown to be asymptomatic carriers with colonization rates as high as 50%.

If a single screen result is negative, a second specimen should be submitted if there is ongoing clinical illness and alternative diagnosis has not been made.

If a single confirmatory result is negative or invalid, testing may be repeated:

  • if clinical status deteriorates or 
  • to diagnose a relapse of CDI following a period of absence of symptoms.

Test of cure for CDI is not recommended. Toxin may persist in stool despite resolution of illness for weeks to months. In the absence of recurrent symptoms, laboratory testing is not helpful in making clinical decisions about patient treatment or precautions.

For surveillance/outbreak related investigations of C. difficile, contact the PHOL Customer Service Center at 416-235-6556 or 1-877-604-4567.


Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit

C. difficile Screen Test

Loose or watery stool

10-15 ml1,2

Sterile container without preservative – Kit Order # 390054

Submission and Collection Notes


Collect a minimum of 10. 0 ml of liquid faeces. DO NOT overfill.


Follow the instructions found in the Clostridioides difficile Kit Instruction Sheet.

Formed stool specimens are the number one rejection reason for C. difficile testing at PHOL and can be as high as 50% for some laboratories.

A Stool Consistency Chart with Acceptance Criteria for Clostridioides difficile Testing is available in English and French to ensure specimens submitted are not rejected. Please share with your patients if they are self-collecting.



Only one sample per patient is tested per collection date.

Storage and Transport

Label the specimen container with the patient’s full name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. Failure to provide this information may result in rejection or testing delay.

Special Instructions

Specimens should be stored at 2-8°C following collection and shipped to PHOL on ice packs. Specimens must be received within 72 hours of collection for optimal testing.

Note: Freezing of the specimen is not required.  Final test results may be affected by freezing and thawing, and may not be accurate.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

The Clostridioides difficile screen test is performed Monday to Saturday. Confirmatory testing is performed within 24 – 48 hours of a positive screen test or the next business day on weekends and holidays.

Turnaround time is up to 3 days from receipt at the PHO laboratory.

Test Methods

Stool specimens are tested by a two-step laboratory screen and confirmatory test process.  

Step one – PHOL – regional sites will screen all stool specimens that meet the acceptance criteria for glutamate dehydrogenase (GDH) antigen and toxins A/B with a rapid enzyme immunoassay.  PHOL – Toronto site will screen stool specimens for GDH antigen with an enzyme immunoassay method.  The difference in test method for the screening test is based on the volume of specimens received at each laboratory site within PHO.

Step two – All stool specimens that require confirmatory testing (refer to the Interpretation Guide for C. difficile on page 3) will be tested for C. difficile toxin gene with a molecular LAMP (loop-mediated isothermal DNA amplification) assay. This testing is performed at a number of PHOL locations in order to optimize the testing turn-around time.

The assay detects a pathogenicity locus (PaLoc) of toxigenic Clostridioides difficile by targeting a partial DNA fragment on the Toxin A gene.  The tcdA target region was selected as an intact region remaining in all known A+B+ and A-B+ toxinotypes. Manufacturer’s sensitivity and specificity performance characteristics as compared to cytotoxic bacterial culture except for the C.DIFF QUIK CHEK COMPLETE Toxin which is compared to tissue culture assay.

  Sensitivity Specificity
(85.7 – 93.9%)
(91.2 – 94.7%)
(81.4 – 92.3%)
(98.6 – 99.7%)
 C.DIFF CHEK-60 70.5%
(60.7 – 78.8%)
(88.5 – 93.4%)
 illumigene C.difficile 95.2%
(89.2 – 97.9%)
(93.2 – 96.7%)


Results are reported to the ordering physician or health care provider as indicated on the requisition.

Data and Analysis

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Laboratory Services

Updated 20 July 2020