Trypanosoma cruzi (Chagas Disease) – Microscopy and PCR

Background
This page provides microscopy and PCR testing information for Chagas disease at Public Health Ontario (PHO). The causative agent of Chagas disease is the parasitic hemoflagellate Trypanosoma cruzi.

Updates
This new test information page was published on October 10, 2025 and includes information that was previously found in Trypanosoma American or African-Serology and Trypanosoma-Microscopy and PCR.

* Copie d'impression non contrôlée. Valide uniquement le jour de l'impression : 10 oct. 2025.

Testing Indications

Trypanosoma cruzi microscopy and PCR should be considered for the diagnosis of individuals with clinical and epidemiological evidence of acute, congenital, or reactivated Chagas disease. Microscopy and PCR are also performed for monitoring of reactivation in instances of known Chagas disease following immunosuppression.¹

For the diagnosis of chronic Chagas disease or for the screening of asymptomatic individuals, microscopy and PCR are not routinely recommended, instead refer to Trypanosoma cruzi (Chagas Disease) – Serology.

Acceptance/Rejection Criteria

T. cruzi microscopy and PCR will only be accepted in cases with any of the following documented:

Travel to a Latin American region (including Mexico, Central America, and South America)
Family history of known Chagas disease
Transplantation, transfusion, or congenital exposure

Failure to provide this information will result in test cancellation or testing delays.

Specimen Collection and Handling

Specimen Requirements

Test Requested	Required Requisition(s)	Specimen Type	Minimum Volume	Collection Kit
Trypanosoma cruzi microscopy	General Test Requisition	Whole blood in EDTA (see special instruction) Unstained, unfixed thick smear Unstained, methanol-fixed thin smear	4.0 ml 2 slides 2 slides	EDTA tube Slide mailer (each slide individually labelled) Slide mailer (each slide individually labelled)
Trypanosoma cruzi microscopy	General Test Requisition	Chagoma skin biopsy	N/A	Sterile container
Trypanosoma cruzi microscopy	General Test Requisition	Lymph node aspirate	1.0 ml	Sterile container
Trypanosoma cruzi microscopy	General Test Requisition	Cerebrospinal fluid (CSF)	1.0 ml	Sterile container
Trypanosoma cruzi microscopy	General Test Requisition	Tissue biopsy	N/A	Sterile container
Trypanosoma cruzi PCR	General Test Requisition	Whole blood in EDTA (see special instruction)	4.0 ml	EDTA tube
Trypanosoma cruzi PCR	General Test Requisition	Chagoma skin biopsy	N/A	Sterile container
Trypanosoma cruzi PCR	General Test Requisition	Lymph node aspirate	1.0 ml	Sterile container
Trypanosoma cruzi PCR	General Test Requisition	Cerebrospinal fluid (CSF)	1.0 ml	Sterile container
Trypanosoma cruzi PCR	General Test Requisition	Tissue biopsy	N/A	Sterile container

Submission and Collection Notes

Complete all fields of the requisition form.

Specify any of the following testing indications on the requisition. Failure to provide this information may result in rejection:

Documented travel history to a Latin American region
Family history of Chagas disease
Transplantation, transfusion, or congenital exposure

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 test cancellation or testing delay.

Timing of Specimen Collection

In cases of congenital Chagas disease, parasitemia levels may be low at birth and peak around 30 days of life, therefore newborns with negative microscopy and PCR results may require repeat testing one month later.

Storage and Transport

Place specimen into the appropriate collection container and securely seal it. Then, insert the sealed container into a biohazard bag and ensure the bag is properly sealed. Specimens should be stored at 2–8°C and shipped to PHO on ice packs within 48 hours of collection. All specimens must be shipped in accordance to the Transportation of Dangerous Good Act.

Special Instructions

For congenital Chagas disease specimen collection, umbilical cord blood or neonate venous blood is preferable to collect. See timing of specimen collection above.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

T. cruzi microscopy is performed Monday to Friday at PHO’s Toronto laboratory site. Turnaround time is up to 4 calendar days from receipt at PHO’s laboratory-Toronto.

T. cruzi PCR is forwarded to the National Reference Centre for Parasitology (NRCP) in Montreal. Turnaround time is up to 28 calendar days from receipt at PHO’s laboratory.

Test Methods

T. cruzi microscopy is performed at PHO using Giemsa staining. Whole blood specimens undergo buffy coat concentration. T. cruzi PCR is performed at the NRCP using a laboratory-developed test that qualitatively amplifies a family of DNA repeats constituting approximately 9% of the nuclear DNA of T. cruzi.

Performance and Limitations:
For blood microscopy, sensitivity following concentration ranges from 40–90% in acute infections, and specificity approximates 100%.² Microscopic parasitemia may be low in the initial days following acute infection and usually peaks 20 to 30 days later followed by a decrease to submicroscopic levels within 90 days. Microscopy sensitivity is low in chronic or early congenital Chagas infections.

For PCR testing, the NRCP assay performance has a stated sensitivity of 85% and specificity of 100%, while other assays have a reported sensitivity of 82-88% and specificity of 98–99% in acute infections. PCR sensitivity in chronic infections is reportedly reduced to 65–89%.³ PCR may be positive prior to microscopy during acute infection and may remain intermittently positive (but is often negative) in chronic infection, therefore a single positive PCR result does not confirm reactivation, and a single negative PCR result does not rule out chronic infection. Quantitative PCR testing is not available in Ontario currently.

Interpretation

For microscopy performed at PHO:

Parasite Microscopy	Identified Organism(s)	Interpretation
Parasite(s) found.	Trypanosoma cruzi trypomastigotes (in fluids) or amastigotes (in tissues).	Detectable T. cruzi organisms by microscopy.
No parasites found.	None.	No detectable T. cruzi organisms by microscopy.

For T. cruzi PCR performed at NRCP:

T. cruzi PCR Result	Interpretation
Negative	No detectable Trypanosoma cruzi DNA.
Indeterminate	Inconclusive result. May be due to a low level of target genetic material in the sample, inadequate sample content, or a non-specific signal. Please resubmit another specimen for testing if clinically indicated.
Positive	Detectable Trypanosoma cruzi DNA. Cannot distinguish acute from chronic infection.
Invalid	Test results are invalid due to the failed detection of the assay controls. May be due to inadequate sample content, extraction failure or test inhibition. Please resubmit another specimen for testing if clinically indicated.

Reporting

Results are received back at PHO, and reports are forwarded to the ordering physician or authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

References

Bern C. Chagas' Disease. N Engl J Med. 2015 Jul 30;373(5):456-66. doi: 10.1056/NEJMra1410150.
Bisio MMC, Rivero R, Gonzalez N, Ballering G, D'Amico I, Kessler C, Moroni S, Moscatelli G, Ruiz AM, Altcheh J. Diagnostic Accuracy of Two Molecular Tools for Diagnosis of Congenital Chagas Disease. Mol Diagn Ther. 2021 Nov;25(6):791-801. doi: 10.1007/s40291-021-00553-3.
Pascual-Vázquez G, Alonso-Sardón M, Rodríguez-Alonso B, Pardo-Lledías J, Romero Alegría A, Fernández-Soto P, Muñoz Bellido JL, Muro A, Belhassen-García M. Molecular diagnosis of Chagas disease: a systematic review and meta-analysis. Infect Dis Poverty. 2023 Oct 16;12(1):95. doi: 10.1186/s40249-023-01143-7.