Clostridioides difficile – Culture and Pulse Field Gel Electrophoresis (PFGE) Typing

Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.

Specimen Collection and Handling

Specimen Requirements

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

C. difficile culture and PFGE typing1,2

Unpreserved stool, no greater than 72 hours old or fresh-frozen faeces

5 ml of liquid faeces (must take the shape of the container)

Sterile container, order #390054

Submission and Collection Notes


Clostridioides difficile PFGE typing is performed for outbreak and cluster investigations only.


Molecular typing for other special circumstances must be approved by a PHOL microbiologist; contact PHOL customer service at 416-235-6556 or 1-877-604-4567.


Include the outbreak number and index case if applicable on the requisition.


Testing laboratories should store positive Clostridioides difficile samples frozen at -20˚C for a minimum of two months to enable retrospective typing, should the need arise.

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

Unpreserved specimens should be transferred to Public Health Ontario Laboratory, Toronto within 72 hours of collection.

Specimens that will exceed the 72 hour cutoff should be stored at -20°C and ship frozen on ice packs. Repeated thawing and freezing of stool should be avoided.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Clostridioides difficile culture and PFGE typing are performed Monday to Friday.

Turnaround time is up to 15 days from receipt by the PHO laboratory.

Test Methods

The following specialized tests are performed for positive C. difficile cultures

  • PFGE typing
  • Specialized toxin typing by Polymerase Chain Reaction, PCR (includes binary toxin elaborated by the ‘hypervirulent” NAP 1 strain) 


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

Data and Analysis

Additional Information

Clostridioides difficile PFGE testing is only performed in outbreak situations.  Indication of the index case is highly recommended.  Molecular typing for special circumstances must be approved by a PHOL Microbiologist at416-235-6556or1-877-604-4567.

Positive Clostridioides difficile toxin samples should be held frozen at -20 °C  for a minimum of two months to enable retrospective typing should the need arise.

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Laboratory Services

Updated 4 Nov 2021