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Species identification of invasive yeasts including Candida in Pakistan: limitations of phenotypic methods
Joveria Farooqi1, Kauser Jabeen, Noureen Saeed
1Department of Pathology & Microbiology, Aga Khan Hospital, Karachi. joveria.farooqi@aku.edu
Objective:
To compare phenotypic and genotypic methods of yeast identification.
Methods:
The in-vitro cross-sectional study was conducted from January 2006 to May 2009. Invasive yeasts isolated at the clinical microbiology laboratory at the Aga Khan University (AKU), Karachi, Pakistan, were identified. Speciation by phenotypic and molecular methods was compared. All yeasts isolated during the study period from blood and other invasive sites were identified using standard methods. Isolates were shipped to Mycotic Diseases Branch, Centres for Disease Control and Prevention, Atlanta, Georgia, USA, for identification by Luminex flow cytometric multianalyte profiling (xMAP) system. Ribosomal ITS2 DNA sequencing was performed on isolates not identified by Luminex.
Result:
Of the 214 invasive yeasts evaluated, Candida species were 209 (97.7%) while the frequency of non-Candida species was 5 (2.3%). Overall agreement between phenotypic and molecular identification was 81.3%, 90.3% amongst the more common Candida species, and only 38.8% amongst the uncommon yeasts.
Conclusion:
Phenotypic methods of identification proved adequate for common Candida species, but were deficient in recognising rare Candida and non-Candida yeasts, highlighting the importance of molecular methods for identification.
Insights
Phenotypic yeast identification is adequate for common Candida species but struggles with rare or non-Candida yeasts. Molecular methods are crucial for accurate identification of all yeast types.
Area of Science:
- Medical Mycology
- Clinical Microbiology
- Infectious Diseases
Background:
- Accurate identification of invasive yeasts is critical for effective patient management.
- Traditional phenotypic methods have limitations in differentiating closely related or rare yeast species.
Purpose of the Study:
- To compare the accuracy of phenotypic and genotypic methods for identifying invasive yeasts.
- To evaluate the performance of molecular techniques against standard identification methods.
Main Methods:
- In vitro cross-sectional study involving 214 invasive yeast isolates.
- Comparison of phenotypic identification with Luminex (xMAP) and ribosomal ITS2 DNA sequencing.
- Isolates were sourced from blood and other invasive sites at Aga Khan University.
Main Results:
- Overall agreement between phenotypic and molecular methods was 81.3%.
- Agreement was higher for common Candida species (90.3%) but significantly lower for uncommon yeasts (38.8%).
- Candida species constituted 97.7% of the isolates; non-Candida species were 2.3%.
Conclusions:
- Phenotypic methods are sufficient for common Candida species identification.
- Molecular methods are essential for accurate identification of rare Candida and non-Candida yeasts.
- Genotypic techniques enhance diagnostic capabilities in clinical microbiology.
