Cyclospora - Subtyping

This document provides testing information for Cyclosopra subtyping at Public Health Ontario. All positive Cyclospora specimens should be sent to PHO’s laboratory for subtyping surveillance and to identify potential sources of outbreaks.

This page is specific to subtyping of known Cyclospora positive specimens. For primary testing of patients suspected of cyclosporiasis, please refer to the following link:

Testing Indications

Cyclospora subtyping is routinely performed on all unpreserved specimens positive for Cyclospora in Ontario. All cases identified on preserved specimens should undergo repeat collection using unpreserved specimens as soon as possible to assist in public health investigations.

Acceptance/Rejection Criteria

Cyclospora subtyping will only be accepted if both of the following conditions are met:

  • Specimen already known to be positive for Cyclospora (e.g. by microscopy or molecular methods).
  • Unpreserved specimen or specimen in Cary-Blair transport medium.

NOTE: specimens preserved in formalin or SAF (e.g., yellow or red top vial) are NOT acceptable for subtyping.

Specimen Collection and Handling

Specimen Requirements

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

Cyclospora subtyping, genotyping, sequencing, or surveillance

Unpreserved stool positive for Cyclospora

0.5 grams

Sterile container, or container with Cary-Blair transport medium (SAF is unacceptable)

Cyclospora subtyping, genotyping, sequencing, or surveillance

Unpreserved duodenal contents or tissue/biopsy materials positive for Cyclospora


Sterile container, or container with Cary-Blair transport medium (SAF is unacceptable)

Submission and Collection Notes


Complete all fields of the General Test Requisition, including:

  1. Write Cyclospora subtyping in the ‘Test(s) Requested’ field.
  2. Specify date of collection in ‘Date Collected” field.
  3. If person travelled, indicate where and when under ‘Recent Travel (Specify Location)’ field.
  4. If part of an outbreak investigation, indicate in the “Public Health Outbreak No.” field

Label the specimen container(s) with the patient’s first and last 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.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Cyclospora subtyping is forwarded to the National Microbiology Laboratory (NML). Results are made available to national and provincial epidemiologists for cluster investigations and outbreak response.

Test Methods

Method: Cyclospora subtyping is performed at NML using targeted amplicon deep sequencing (TADS) as per Yanta et al. (2022)1 and based on a similar US Centers for Disease Control and Prevention (US CDC) protocol. Temporal-genetic cluster codes are assigned based on genotypic relatedness and date of collection for national response.

Performance and Limitations: Sequencing methods are currently undergoing validation and used for epidemiological surveillance and outbreak investigations only. Results are not actionable for clinical management.


Results will be finalized as “Sample received for surveillance purposes, no further result to report” with no further results provided directly to submitters.


At this time, sequencing results will only be made available to PHO and Public Health Agency of Canada (PHAC) epidemiologists through the Canadian Network for Public Health Intelligence (CNPHI) for cluster investigations. A generic confirmation of receipt will be provided to the specimen submitter as indicated on the requisition.


  1. Yanta CA, Barta JR, Corbeil A, Menan H, Thivierge K, Needle R, Morshed M et al. Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations. Microorganisms. 2022 Feb; 10(2): 447. Available at:
Mis à jour le 25 juin 2024