Changes to Stool Testing at Public Health Ontario Laboratory

To: Ottawa Physicians and Nurse Practitioners
Date: January 5, 2026
From: Dr. Michelle Foote, Associate Medical Officer of Health
Subject: Changes to Stool Testing at Public Health Ontario Laboratory

Dear Colleagues,

The following information has been summarized from an email (only available in English) from Public Health Ontario (PHO).

On December 15, 2025, PHO implemented a molecular detection assay (PCR) to replace microscopy for detecting enteric protozoa in stool specimens. The new PCR panel detects 5 protozoa: Cryptosporidium, Cyclospora, Dientamoeba fragilis, Entamoeba histolytica, and Giardia duodenalis.

Specimen submissions for PCR will ONLY be tested if the requisition indicates any of the following, otherwise submissions will be cancelled:

• Signs or symptoms consistent with enteric protozoal infection (e.g., diarrhea)
• Close contact of an infected person (e.g., household or outbreak cluster)

Acceptable Specimens for PCR: Stool in a Cary-Blair medium (e.g., Copan FecalSwab or another Cary Blair medium). Alternatively, unpreserved stool in a sterile empty vial is acceptable but is less preferable.

Unacceptable Specimens for PCR: Stool in SAF (sodium acetate, acetic acid, formalin) is NOT suitable for PCR and will be cancelled.

Microscopy will remain available for parasites not included in the PCR panel such as other apicomplexans (e.g., Cystoisospora, Sarcocystis), Balantioides, helminths (e.g., ova, larvae), microsporidia (e.g. Enterocytozoon, Encephalitozoon), and visible worms. Microscopy will ONLY be performed if the requisition indicates any of the following, otherwise submissions will be cancelled:

• Impaired immune system (e.g., HIV, transplant, steroids)
• International travel or migration
• Livestock exposure (e.g., farmer)
• Undercooked seafood, amphibian, reptile, or gastropod ingestion
• Unexplained eosinophilia
• Known positive serological test for a parasitic infection (specify which organism)
• Close contact of an infected person (e.g., household or outbreak cluster)

Important: Effective January 31, 2026, all microscopy submissions without the above indications will be cancelled. Cancellations will require recollection and resubmission of another stool specimen with appropriate indication(s) on the requisition if microscopy is still clinically indicated.

Acceptable Specimens for Microscopy: Stool in an SAF vial. The requisition should indicate which type of organism is suspected (e.g., apicomplexan, helminth, and/or microsporidia) based on the clinical presentation and exposure history.

Unacceptable Specimens for Microscopy: Stool in Cary Blair medium or unpreserved vial is NOT suitable for microscopy and will be cancelled.

For additional testing information please refer to the following test information on the PHOL webpages:

• Enteric Protozoa (Cryptosporidium, Cyclospora, Dientamoeba, Entamoeba, and Giardia) – PCR
• Enteric Helminths (Nematodes, Trematodes, Cestodes, Acanthocephalans) and Balantioides - Microscopy
• Microsporidia (Microsporidiosis) – Microscopy and PCR
• Sarcocystis (Sarcocystosis) – Microscopy
• Cystoisospora (Cystoisosporiasis) – Microscopy
• Enterobius (Pinworm) – Microscopy
• Clonorchis (Clonorchiasis) – Microscopy and Antibody
• Fasciola (Fascioliasis) – Microscopy and Antibody
• Paragonimus (Paragonimiasis) – Microscopy and Antibody
• Schistosoma (Schistosomiasis) – Microscopy, Antibody, and Antigen
• Strongyloides (Strongyloidiasis) – Microscopy and Antibody
• Taenia solium (Cysticercosis) – Antibody and PCR
• Extraintestinal Entamoeba histolytica (Amebic Abscess) - Microscopy, PCR, and Antibody
• Worm (Whole or Segment) – Identification

For questions regarding information on any of the above testing information, please call PHO’s Laboratory Customer Service Centre at 1-877-604-4567 (toll free) or 416-235-6556, or email CustomerServiceCentre@oahpp.ca.