Mycology – Anti-Fungal Susceptibility Testing of Yeast and Filamentous Fungi
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.
This page provides testing information for anti-fungal susceptibility testing (AFST) of yeasts and filamentous fungi at Public Health Ontario (PHO).
For information regarding other testing options, refer to the following PHO webpages:
- Mycology – Fungal Culture - Superficial
- Mycology – Nocardia and Aerobic Actinomycetes culture
- Mycology – Antimicrobial susceptibility testing of Nocardia and Aerobic Actinomycetes
- Mycology – Pneumocytis jirovecii (PJP) detection
- Mycology – Reference Identification of Yeasts, Filamentous Fungi and Nocardia/Aerobic Actinomycetes
Updates
- Testing indication for susceptibility testing of yeast isolates versus filamentous fungi have been clearly separated. Refer to testing indications section below.
- Isavuconazole breakpoints are now available for Apergillus fumigatus sensu stricto. Refer to the interpretation section below.
Testing Indications
Yeast:
- Susceptibility testing for yeast will be performed from sterile sites only; exceptions can be made for isolates from non-sterile sites from patients that are immunocompromised, in the ICU or experiencing treatment failure.
- Susceptibility testing of Candida albicans is currently restricted to immunocompromised patients, patients in the ICU, post-transplant patients or with evidence of treatment failure.
Filamentous Fungi:
- Susceptibility testing for filamentous fungi is not routinely performed and requires a consultation with and approval by the PHO Microbiologist that oversees Mycology prior to sending isolates.
- Please contact PHO’s Laboratory Customer Service Center at 1-877-604-4567 or 416-235-6556 for exceptions and pre-approvals when sending isolates that do not fulfill the testing indications above.
Acceptance/Rejection Criteria
Isolates must be received as pure culture only. Samples received in a mixed/contaminated state will be cancelled upon receipt. If a lab is unable to isolate a pure culture of the fungus under investigation they should consider submitting appropriate direct specimens for Fungal Culture to PHO Mycology Laboratory, or should contact the PHO Microbiologist that oversees Mycology to discuss.
Isolates of Candida albicans submitted without required testing indications as mentioned above, will be cancelled and referred to Provincial susceptibility data for Candida albicans (2014-2018) showing its usual susceptibility to all antifungal agents.
For yeast isolates repeatedly isolated from the same patient, susceptibility testing is performed up to one time per week. Requests for repeat susceptibility testing within <7 days of each other will be cancelled and referred back to the previous yeast isolate’s susceptibility testing results.
Specimen Requirements
| Test Requested | Required Requisition(s) | Specimen Type | Minimum Volume | Collection Kit |
AFST – Yeast isolate |
Pure culture of yeast isolate |
N/A |
Appropriate culture media for growth (slant or plate) or Swab from pure culture (see note # 3 below) |
|
AFST – filamentous fungi isolate (PHO microbiologist approval required prior to submission) |
Pure culture of filamentous fungus isolate |
N/A |
Appropriate culture media for growth (slant or plate) or Swab from pure culture (see note # 3 below) |
Submission and Collection Notes
Complete all fields of the requisition form, fields a-d are mandatory:
- Test(s) requests and indications for testing
- Patient setting/population/source
- Pre-approval given by (where required):
Note: For filamentous fungi susceptibility requests, indicate prior approval given by the PHO Microbiologist on requisition. - Immune status – REQUIRED - important to note on the requisition if patient is in ICU, has had a transplant, has a haematological malignancy, or is otherwise immunocompromised etc. as this will impact approval for testing.
- Organism identification must be provided or requested by the submitting laboratory.
- Any special drug requests – these must be discussed with the Microbiologist prior to submission.
Label the isolate’s container(s) with the patient’s first and last name, date of collection of the original specimen, and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.
Place isolate in a biohazard bag and seal. Store cultures at room temperature or 28°C until submitted. Specimens should be shipped to PHO’s laboratory as soon as possible.
Limitations
Culture must be submitted in pure state. Isolates received in a mixed/contaminated state will result in cancellation.
Storage and Transport
Specimens should be stored at room temperature or 28°C following collection and shipped to PHO’s laboratory as soon as possible. All clinical specimens must be shipped in accordance to the Transportation of Dangerous Good Act.
Test Frequency and Turnaround Time (TAT)
The antifungal susceptibility is done at PHO’s Toronto laboratory, with the following frequency:
- Candida spp.: set up daily from Monday to Thursday
- Cryptococcus neoformans complex and other non-Candida yeast: set up on Mondays, Tuesdays and Fridays
- Aspergillus spp. and other rapid growing organisms (such as Mucorales): set up on Mondays, Tuesday and Wednesdays
- Other filamentous fungi: set up on Mondays, Tuesday and Wednesdays
Turnaround time for susceptibility testing from pure culture organisms, after receipt by the PHO – Toronto laboratory is:
- Candida spp.: within 5 working days
- Cryptococcus neoformans complex and other non-Candida yeast: within 7 working days
- Aspergillus spp. and other rapid growing organisms (such as Mucorales): within 7 working days
- Other filamentous fungi: variable turnaround time (see note below)
NOTE: The TAT for filamentous fungi can vary greatly from organism to organism and is dependent on organism sporulation at 35°C. CLSI guidelines indicate filamentous fungus should be incubated to develop sporulation for up to 7 days prior to setting up antifungal susceptibility micro broth dilution panels.
Antifungal susceptibility testing of yeasts and filamentous fungi are performed by microbroth dilution and is a fully compliant to Clinical and Laboratory Standards Institute method. Interpretations are reported where available according to CLSI M27M44S and CLSI M38M51S.
Results reported as ‘No Interpretation’ indicate that CLSI has not developed any accepted clinical breakpoints to determine susceptibility or resistance.
Drugs not available in house may be available by special request. Consult the PHO Microbiologist that oversees Mycology to discuss prior to submitting. Susceptibility testing for drugs not available on in house panels may result in referral to an outside laboratory.
Antifungal Susceptibility Testing on dimorphic fungi is not available.
Algorithm
|
Organism Group |
Susceptibility testing |
Drugs Tested |
Notes |
|---|---|---|---|
|
Candida yeasts
|
Routinely performed on isolates from sterile sites only.
For isolates from non-sterile site requires pre-approval from PHO Microbiologist. |
Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin) Azoles (fluconazole, itraconazole, posaconazole and voriconazole) 5-Flucytosine |
Candida albicans testing available only for immunocompromised patients, patients in ICU, post-transplant or with evidence of treatment failure. Pre-approval is required. |
|
Cryptococcus Rhodotorula Saccharomyces (and other |
Routinely performed on isolates from sterile sites only.
For isolates from non-sterile site requires pre-approval from PHO Microbiologist. |
Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin) Azoles (fluconazole, itraconazole, posaconazole and voriconazole) 5-Flucytosine |
Not all drugs are reported routinely.
Drugs reported may be dependent on organism and applicable CLSI guidelines. |
|
Filamentous fungi |
Pre-approval is required from PHO Microbiologist.
Testing is typically reserved for patients with underlying malignancies, immune complications, transplant and other complicating factors. |
Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin) Azoles (fluconazole, itraconazole, posaconazole, voriconazole and isavuconazole) 5-Flucytosine |
Requests for susceptibility testing that are received without prior approval are subject to cancellation. |
Interpretation
The following table provides possible test results with associated interpretations:
|
Organism |
Result |
Comments |
|---|---|---|
|
Candida yeasts |
MIC values and interpretations are routinely reported for: Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin) Azoles (fluconazole, itraconazole, posaconazole and voriconazole) |
Interpretations reported are based on CLSI M27M44S and are available for some drugs and the most commonly isolated Candida spp.
Reporting of some drugs may be restricted dependent on body site, as per CLSI M27M44S. |
|
Cryptococcus
|
MIC values are reported for: Amphotericin B 5-flucytosine Azoles |
There are no MIC interpretations available for these organisms, as per CLSI.
Reporting of some drugs may be restricted dependent on body site or intrinsic resistance, as per CLSI M27M44S. |
|
Rhodotorulla Saccharomyces (and other |
MIC values are reported but may be organism dependent:
Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin)
Azoles (fluconazole, itraconazole, posaconazole, voriconazole and isavuconazole) 5-Flucystosine |
There are no MIC interpretations available for these organisms, as per CLSI.
Reporting of some drugs may be restricted dependent on body site or intrinsic resistance, as per CLSI M27M44S. |
|
Filamentous fungi |
MIC/MEC values are reported but may be organism dependent:
Amphotericin B Echinocandins (anidulafungin, micafungin and caspofungin)
Azoles (fluconazole, itraconazole, posaconazole, voriconazole and isavuconazole) 5-Flucystosine |
Currently,only Aspergillus fumigatus sensu strictu has established breakpoints for voriconazole and isavuconazole as per CLSI M38M51S. For all other organisms/drugs there are no MIC interpretations available for as per CLSI. |
MIC = minimal inhibitory concentration
MEC = minimal effective concentration
Reporting
Results are reported to the physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.
References
- Clinical and Laboratory Standards Institute, M54 Principles and Procedures for Detection and Culture of Fungi in Clinical Specimens, 2nd Ed., CLSI, January 2021
- Clinical and Laboratory Standards Institute, M27M44S Performance Standards for Antifungal Susceptibility Testing of Yeasts, 4th Ed., CLSI, March 2026
- Clinical and Laboratory Standards Institute, M38M51S Performance Standards for Antifungal Susceptibility Testing of Filamentous Fungi, 4th Ed., CLSI, March 2026
- Leber, A.L., Burnham, CA.D. Clinical Microbiology Procedures Handbook, 5th Edition, American Society for Microbiology; John Wiley & Sons, Inc., 2023.
- de Hoog, G.S., et al, Atlas of Clinical Fungi, 4th Ed. Foundation Atlas of Clinical Fungi, Hilversum, 2020
MyPHO
Don’t have a MyPHO account? Register Now