
Mycology - Fungal Culture - Systemic
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.
Background
This page provides testing information for systemic fungal cultures at Public Health Ontario (PHO). This page is for information specific to fungal cultures from systemic sources such as fluids, tissues, blood, respiratory secretions, tissues, abscess etc. For information regarding other mycology-related testing options, please refer to the following PHO webpages:
- Mycology - Fungal Culture – Superficial, Dermatophytes
- Mycology - Nocardia and Aerobic Actinomycetes culture
- Mycology - Pneumocytis jirovecii (PJP) detection
- Mycology - Reference Identification – Yeast, Filamentous Fungi, Nocardia and Aerobic Actinomycetes
- Mycology – Antifungal Susceptibility Testing of Yeast and Filamentous Fungi
- Mycology – Antimicrobial Susceptibility Testing (AST) of Nocardia and Aerobic Actinomycetes
Updates
- This update reflects a change in organization from specimen type to test type. The following former TISs have been merged into this update:
- Fungal infections – external ear
- Fungus culture – Blood and Bone Marrow
- Fungus Culture – Body Fluids
- Fungus Culture – CSF
- Fungus culture – Eye
- Fungus culture – Respiratory
- Fungus culture – Subcutaneous
- TIS pages for systemic fungal culture were previously organized by body type/specimen source.
- The following labstract(s) have been removed and information is included in this document:
- LAB-SD-S- 050 Systemic Mycoses – Change in Specimen Submission Guidelines
- LAB-SD-022 Fungal Blood Culture Requests
- Submit a separate specimen and requisition for mycology testing regardless of what additional testing is requested e.g. if fungal culture and TB/Mycobacteria or Legionella culture are required, separate specimens and requisitions should be submitted for each.
Testing Indications
To establish the presence of yeast, filamentous fungi and dimorphic pathogens from clinical specimens. Appropriate specimens should be collected when fungal infections are being considered.
Acceptance/Rejection Criteria
Samples will be subject to rejection/cancellation under the following circumstances:
- Specimen submitted as one sample/one requisition with requests for multiple test types
- Requests for both fungal culture and Pneumocystis microscopy may be submitted using the same specimen and requisition.
- Specimens that have leaked in transit
- Improper submission eg. specimen in VTM, formalin or other UTM
- Stool specimen for fungal testing (including yeast) are not routinely tested except in cases involving neonates or severely immunocompromised patients who are hospital inpatients.
- Vaginal swabs for the investigation of vaginal candidiasis are not accepted. Culture is reserved for cases of recurrent infection, treatment failure and other indications on special request only.
Specimen Collection and Handling
If volume/quantity is sufficient, a direct microscopic exam is automatically included for samples submitted for fungus culture (with the exception of blood and bone marrow specimens).
Failure to include details on patient setting and immune status will result in limited work-up of organisms from non-sterile sites (eg. respiratory sources). To ensure delays are limited, complete all areas of the requisition in as much detail as possible (see below).
Specimen Requirements
Test Requested | Required Requisition(s) | Specimen Type | Minimum Volume | Collection Kit |
Fungal Culture |
Blood |
1-5 ml |
ONLY |
|
Fungal Culture |
Body Fluids - Pleural, ascites, joint, vitreous |
1.0-2.0 mL |
Sterile container |
|
Fungal Culture |
Cerebrospinal fluid |
1.0 mL |
Sterile container |
|
Fungal Culture |
Ear (material collected from ear canal) |
none |
Collect material using a curette or dry swab or swab in charcoal or Amies transport media. |
|
Fungal Culture |
Eye (Biopsy, corneal scrapings, enucleation, ulcers, keratitis, intraocular fluid, vitreous/aqueous eye fluid, lacrimal gland/canal, anterior chamber fluid, washing fluid) |
none |
Sterile container Swabs are NOT a suitable specimen |
|
Fungal Culture |
Respiratory secretions – bronchial washings, sputum, bronchial alveolar lavage. |
1.0 mL |
Sterile container |
|
Fungal Culture |
Subcutaneous tissue (Skin ulcers, biopsy/autopsy materials, surgically collected sinus wall scrapings, tissues, bone marrow) |
Approx. 3 mm x 3mm |
Sterile container (Swabs discouraged) For skin ulcers, biopsies are preferable to swabs since the presence of fungal elements within tissues is a diagnosis of invasive disease. The biopsy should be taken near the periphery of the lesion and should include enough tissue for culture. |
Submission and Collection Notes
Complete all fields of the requisition form, including:
- Test(s) requests and indications for testing
- Specimen source (with details)
- Collection date and time
- Patient setting (eg. out-patient, in-patient, ICU, burn ward etc) - VERY important to note on the requisition
- Current antifungal therapy and/or clinical diagnosis.
- Immune status – VERY important to note on the requisition if patient has had a transplant, has a haematological malignancy, or is otherwise immunocompromised (including burn wounds, diabetes etc) as this will impact work up and reporting practices
- Requests for specific organisms of concern (dimorphics, Aspergillus, Fusarium, Malassezia, risk group 3 pathogens, etc.)
- Any available direct microscopic exam results from submitting lab
For clinical specimens, 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. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.
Submit a separate specimen and requisition for mycology testing, no matter what additional testing is requested, i.e. if fungal culture and TB or Legionella culture are required, separate specimens and requisitions should be submitted for each.
Timing of Specimen Collection
Please submit a maximum of 1 specimen per patient, per site, per day if necessary. Submitting more than one specimen per site may result in samples being pooled, or later specimens being referred to earlier results.
Limitations
Submit a separate specimen and requisition for mycology testing, no matter what additional testing is requested, i.e. if fungal culture and TB/Mycobacteria or Legionella culture are required, separate specimens and requisitions should be submitted for each.
Requests for both fungal culture and Pneumocystis microscopy may be submitted using the same specimen and requisition.
Storage and Transport
Refer to the table below for specimen storage guidelines. Specimens should be shipped to PHO’s laboratory as soon as possible after collection. All clinical specimens must be shipped in accordance to the Transportation of Dangerous Good Act.
Source |
Storage Temp |
Shipping Conditions/Time |
---|---|---|
Blood |
Room temperature |
Samples should be collected at the time of febrile episodes. Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Body Fluids - Pleural, ascites, joint, vitreous |
Room temperature |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Cerebrospinal fluid |
Room temperature |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Ear (material collected from ear canal) |
Room temperature |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Eye (Biopsy, corneal scrapings, enucleation, ulcers, keratitis, intraocular fluid, vitreous/aqueous eye fluid, lacrimal gland/canal, anterior chamber fluid, washing fluid) |
Room temperature |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Respiratory secretions – bronchial washings, sputum, bronchial alveolar lavage. |
Store specimen at 4°C. |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Subcutaneous tissue (Skin ulcers, biopsy/autopsy materials, surgically collected sinus wall scrapings, tissues, bone marrow) |
Room temperature |
Place specimen in a biohazard bag and seal. Specimens should be shipped to the lab ASAP; ideally within 72 hours of collection. |
Special Instructions
For yeasts, susceptibility testing 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.
Note: Susceptibility testing of Candida albicans is currently restricted to immunocompromised patients, patients in the ICU, post-transplant patients or with evidence of treatment failure. For requests outside of these criteria please contact PHO for special request.
For susceptibility testing of filamentous fungi, PHO Microbiologist approval is required. Please contact PHOL Customer Service.
Test Frequency and Turnaround Time (TAT)
Systemic fungal culture test is done daily Monday to Friday at Public Health Ontario Laboratory sites in Toronto and Thunder Bay.
Turnaround Time for microscopy: 2 business days from receipt at PHO Laboratory.
Turnaround Time for culture report: 10 business days (2 weeks) from receipt at PHO Laboratory.
Turnaround Time for Identification of isolates: dependent on the organism(s).
Microscopic exam uses Fungifluor and/or Calcofluor White Stain.
Calcofluor White is a non-specific fluorochrome that binds to the chitin in the cell wall of fungi and fluoresces blue-white under ultraviolet microscopy.
Fungal culture identification uses various conventional methods, including microscopic morphology, biochemical reactions, and growth temperature and culture characteristics. Molecular methods such as qPCR, PCR and sequence analysis and MALDI-TOF MS will be used when needed.
All specimens will be screened for dimorphic fungi (Blastomyces dermatitidis/gilchristii, Histoplasma capsulatum, Coccidioides immitis/posadasii) and Cryptococcus neoformans/gattii.
High Risk (i.e. immunocompromised) individuals will have enhanced identification to genus species level.
- For individuals at high risk of invasive fungal infection (eg. immunocompromised, ICU, burn wound patients, diabetics, transplant patients etc) enhanced identification to the appropriate genus/species level will be provided for respiratory tract (sputum, endotracheal aspirate, bronchial washing, bronchoalveolar lavage), skin (vascular catheter exit site only) and urine specimens.
For non-high risk patients and in cases where no clinical information has been provided, fungal isolation will usually be targeted to the detection and identification of dimorphic fungi and Cryptococcus neoformans/gattii.
For respiratory tract, skin and urine specimens, for example, if a yeast is isolated from any of the above specimens, it will be reported as “Yeast isolated, not Cryptococcus neoformans/gattii” without further identification.
Likewise, if a non-dimorphic filamentous fungus is isolated from a smear-negative specimen, it will be reported as “Filamentous fungus isolated,” without further identification. If the clinician requires further investigation on any isolate or specimen, please seek a consultation with the PHO microbiologist that oversees mycology.
Full identification will be performed on isolates from sterile sites (ie. sterile fluids, blood cultures, tissues, biopsies).
BLOOD: Blood specimens are processed on the BD Bactec system using the Myco/F lytic bottles.
Most fungal blood stream infections are caused by Candida spp. or other yeast, or yeast like organisms, Cryptococcus neoformans, and less frequently Trichosporon, Geotrichum or Rhodotorula. Most yeast (eg. Candida species) will grow in regular blood culture bottles and do not require the use of the Myco/F Lytic system for detection. Comparable recovery of Candida species has been found using a combination of standard aerobic and anaerobic bacterial blood culture bottles compared to the Myco/F Lytic bottles. Please continue to order judiciously.
Malassezia is a yeast that is not optimally detected by automated blood culture systems, and requires special isolation procedures. For suspect Malassezia infections, i.e. central line or parenteral nutrition infections and undiagnosed neonatal sepsis, please note this on the requisition so that special techniques can be applied.
It should be noted that with the exception of Fusarium species, most filamentous fungi are difficult to grow from the blood despite the fact that infections such as disseminated aspergillosis and mucormycosis are spread via the bloodstream. When Aspergillus is isolated from blood cultures, it is more often a contaminant than a true positive.
Algorithm
A direct microscopic exam and culture is performed on all specimens submitted for fungal culture (with the exception of blood and bone marrow specimens in which only culture is performed).
Any specimen in which the direct exam is positive for fungal filaments will receive a full workup.
Culture results are reported within two weeks incubation; the cultures are held up to 4 weeks and you will be notified of any significant late growth.
Interpretation
The following table provides possible test results with associated interpretations:
All specimens will be screened for dimorphic fungi (Blastomyces dermatitidis/gilchristii, Histoplasma capsulatum, Coccidioides immitis/posadasii) and Cryptococcus neoformans/gattii.
Source/Patient | Direct Microscopic Exam | Final Report |
---|---|---|
Non-sterile site Non-high risk patient |
No fungal elements seen Budding yeast (and/or pseudohyphae) seen
Or Fungal elements seen/fungal filaments seen |
Yeast isolated will be reported as ‘Yeast, not Cryptococcus neoformans/gattii’ Filamentous fungi isolated may be reported as ‘filamentous fungi’ or ‘mixture of filamentous fungi’ with an appropriate note.
|
Sterile site Non-high risk patient |
No fungal elements seen Or Fungal elements seen (budding yeast, fungal filaments etc) |
Yeast will be identified to genus/species level.
Filamentous fungi will be identified to genus/species level. |
Non-sterile site High risk patient or Sterile site High risk patient |
No fungal elements seen Or Fungal elements seen |
Yeast will be identified to genus/species level.
Filamentous fungi will be identified to genus/species level. |
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.
Identified isolates that are designated as causing disease of public health significance are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.
References
- Clinical and Laboratory Standards Institute, M54 Principles and Procedures for Detection and Culture of Fungi in Clinical Specimens, 2nd Ed., CLSI, January 2021
- Leber, Amy L.. Clinical Microbiology Procedures Handbook, 4th Ed., American Society for Microbiology, January 2016
- de Hoog, G.S., et al, Atlas of Clinical Fungi, 4th Ed. Foundation Atlas of Clinical Fungi, Hilversum, 2020
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