Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections

Minh Thuy Vi Hoang (1) , Laszlo Irinyi (2) , Sharon Chen (1) , Tania C Sorrell (1) , Wieland Meyer (1) , The Isham Barcoding of Medical Fungi Working Group , Stephane Ranque (3, 4)

1 The University of Sydney
2 CIDM - Centre for Infectious Disease and Microbiology
3 VITROME - Vecteurs - Infections tropicales et méditerranéennes
4 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection

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.

Keywords: identification; fungal DNA barcoding; dual barcoding system; internal transcribed spacer region; translational elongation factor 1α; ISHAM Barcoding Database; invasive fungal diseases

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Bacteriology; Life Sciences [q-bio]; Microbiology and Parasitology; Virology; Life Sciences [q-bio]; Microbiology and Parasitology; Parasitology; Life Sciences [q-bio]; Human health and pathology; Cardiology and cardiovascular system; Life Sciences [q-bio]; Human health and pathology; Emerging diseases; Life Sciences [q-bio]; Human health and pathology; Infectious diseases

Minh Thuy Vi Hoang, Laszlo Irinyi, Sharon Chen, Tania C Sorrell, Wieland Meyer, et al.. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections. Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.01647⟩. ⟨hal-02481964⟩