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Comparison of PCR-RFLP with 21-plex PCR and rDNA Sequencing for Identification of Clinical Yeast Isolates

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Abstract

Non-albicans Candida species and other rare yeasts have emerged as major opportunistic pathogens in fungal infections. Identification of opportunistic yeasts in developing countries is mainly performed by phenotypic assay, which are time-consuming and prone to errors. The aim of the present study was to evaluate PCR-RFLP as a routinely used identification technique for the most clinically important Candida species in Iran and make a comparison with a novel multiplex PCR, called 21-plex PCR. One hundred and seventy-three yeast isolates from clinical sources were selected and identified with sequence analysis of the D1/D2 domains of rDNA (LSU rDNA) sequencing as the gold standard method. The results were compared with those obtained by PCR-RFLP using MspI restriction enzyme and the 21-plex PCR. PCR-RFLP correctly identified 93.4% of common pathogenic Candida species (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and P. kudriavsevii (= C. krusei)) and was able to identify 45.5% of isolates of the uncommon yeast species compared to the D1/D2 rDNA sequencing. Compared with PCR-RFLP, all common Candida species and 72.7% of uncommon yeast species were correctly identified by the 21-plex PCR. The application of the 21-plex PCR assay as a non-sequence-based molecular method for the identification of common and rare yeasts can reduce turnaround time and costs for the identification of clinically important yeasts and can be applied in resource-limited settings.

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Acknowledgements

The authors would like to thank Mohammad Reza Safari and Azar Berahmeh for their assistance during the study.

Funding

This study was part of a PhD. dissertation (grant No. 9511353003) and M.S. dissertation (grant No. 9711352002) supported by Tehran University of Medical Sciences. This study has been funded and supported by Tehran University of Medical Sciences (TUMS); grant no. 99-1-99-46502.

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Authors and Affiliations

  1. Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

    Mohammad Kord, Ahmad Elmimoghaddam, Seyed Jamal Hashemi, Sassan Reziae, Roshanak Daie Ghazvini, Ali Ahmadi, Muhammad Ibrahim Getso & Sadegh Khodavaisy

  2. Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran

    Mohammadreza Salehi

  3. Department of Pathology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran

    Alireza Abdollahi

  4. Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, College of Health Sciences, Bayero University Kano, Kano, Nigeria

    Muhammad Ibrahim Getso

  5. Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands

    Teun Boekhout

  6. Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands

    Teun Boekhout

  7. Scientific research center, Tehran University of Medical Sciences, Tehran, Iran

    Ali Ahmadi

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  1. Mohammad Kord
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Contributions

SK, SJH, RDG, and MK designed the study. AE, SK, MK, and AA collected yeast isolates. MK, MRS, and AA collected clinical data. MK, AE, AA, and MG performed molecular identification. SK, SR, TB, RDG, and SJH performed data analysis. MK, SK, MG, and AE prepared the first draft. All authors contributed in revision.

Corresponding author

Correspondence to Sadegh Khodavaisy.

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Kord, M., Elmimoghaddam, A., Hashemi, S.J. et al. Comparison of PCR-RFLP with 21-plex PCR and rDNA Sequencing for Identification of Clinical Yeast Isolates. Mycopathologia 186, 213–220 (2021). https://doi.org/10.1007/s11046-020-00522-0

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  • DOI: https://doi.org/10.1007/s11046-020-00522-0

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