Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections

Minh Thuy Vi Hoang, Laszlo Irinyi, Sharon C.A. Chen, Tania C. Sorrell, Wieland Meyer, Michael Arabatzis, Ian Arthur, Jose F. Cano-Lira, Gianluigi Cardinali, Laura Rosio Castañón, Wen Chen, Ariya Chindamporn, Arnaldo L. Colombo, Marie Desnos-Ollivier, Wilhelm De Beer, Sybren De Hoog, Westerdijk Fungal, Françoise Dromer, Dea Garcia-Hermoso, Marieka GryzenhoutJosep Guarro, Catriona Halliday, Marijke Hendrickx, Sabine Huhndorf, C. Andre Levesque, Maria Luiza Moretti, Mauro De Medeiros Muniz, Analy Salles De Azevedo Melo, Angela Satie Nishikaku, Anne Cécile Normand, Célia Pais, Renaud Piarroux, Stéphane Ranque, Barbara Robbertse, Vincent Robert, Conrad L. Schoch, Keith A. Seifert, Célia Maria De Almeida Soares, John L. Spouge, Dirk Stubbe, Maria Lucia Taylor, Conchita Toriello, Aristea Velegraki, Chompoonek Yurayart, Rosely Maria Zancopé-Oliveira

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Abstract

Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.
Original languageEnglish
JournalFrontiers in Microbiology
Volume10
Issue numberJULY
DOIs
Publication statusPublished - 2019

Keywords

  • Dual barcoding system
  • Fungal DNA barcoding
  • ISHAM Barcoding Database
  • Identification
  • Internal transcribed spacer region
  • Invasive fungal diseases
  • Translational elongation factor 1α

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