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 Gryzenhout; Josep 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

doi:10.3389/fmicb.2019.01647

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/periodical › Article › Scientific › peer-review

41 Citations (Scopus)

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 language	English
Journal	Frontiers in Microbiology
Volume	10
Issue number	JULY
DOIs	https://doi.org/10.3389/fmicb.2019.01647
Publication status	Published - 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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10.3389/fmicb.2019.01647

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Hoang, M. T. V., Irinyi, L., Chen, S. C. A., Sorrell, T. C., Meyer, W., Arabatzis, M., Arthur, I., Cano-Lira, J. F., Cardinali, G., Castañón, L. R., Chen, W., Chindamporn, A., Colombo, A. L., Desnos-Ollivier, M., De Beer, W., De Hoog, S., Fungal, W., Dromer, F., Garcia-Hermoso, D., ... Zancopé-Oliveira, R. M. (2019). Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections. Frontiers in Microbiology, 10(JULY). https://doi.org/10.3389/fmicb.2019.01647

@article{ae8c6e6f9fc64dc9bbc90af3db080485,

title = "Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections",

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.",

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

author = "Hoang, {Minh Thuy Vi} and Laszlo Irinyi and Chen, {Sharon C.A.} and Sorrell, {Tania C.} and Wieland Meyer and Michael Arabatzis and Ian Arthur and Cano-Lira, {Jose F.} and Gianluigi Cardinali and Casta{\~n}{\'o}n, {Laura Rosio} and Wen Chen and Ariya Chindamporn and Colombo, {Arnaldo L.} and Marie Desnos-Ollivier and {De Beer}, Wilhelm and {De Hoog}, Sybren and Westerdijk Fungal and Fran{\c c}oise Dromer and Dea Garcia-Hermoso and Marieka Gryzenhout and Josep Guarro and Catriona Halliday and Marijke Hendrickx and Sabine Huhndorf and {Andre Levesque}, C. and Moretti, {Maria Luiza} and {De Medeiros Muniz}, Mauro and {De Azevedo Melo}, {Analy Salles} and Nishikaku, {Angela Satie} and Normand, {Anne C{\'e}cile} and C{\'e}lia Pais and Renaud Piarroux and St{\'e}phane Ranque and Barbara Robbertse and Vincent Robert and Schoch, {Conrad L.} and Seifert, {Keith A.} and {De Almeida Soares}, {C{\'e}lia Maria} and Spouge, {John L.} and Dirk Stubbe and Taylor, {Maria Lucia} and Conchita Toriello and Aristea Velegraki and Chompoonek Yurayart and Zancop{\'e}-Oliveira, {Rosely Maria}",

year = "2019",

doi = "10.3389/fmicb.2019.01647",

language = "English",

volume = "10",

journal = "Frontiers in Microbiology",

issn = "1664-302X",

publisher = "Frontiers Media SA",

number = "JULY",

}

Hoang, MTV, Irinyi, L, Chen, SCA, Sorrell, TC, Meyer, W, Arabatzis, M, Arthur, I, Cano-Lira, JF, Cardinali, G, Castañón, LR, Chen, W, Chindamporn, A, Colombo, AL, Desnos-Ollivier, M, De Beer, W, De Hoog, S, Fungal, W, Dromer, F, Garcia-Hermoso, D, Gryzenhout, M, Guarro, J, Halliday, C, Hendrickx, M, Huhndorf, S, Andre Levesque, C, Moretti, ML, De Medeiros Muniz, M, De Azevedo Melo, AS, Nishikaku, AS, Normand, AC, Pais, C, Piarroux, R, Ranque, S, Robbertse, B, Robert, V, Schoch, CL, Seifert, KA, De Almeida Soares, CM, Spouge, JL, Stubbe, D, Taylor, ML, Toriello, C, Velegraki, A, Yurayart, C & Zancopé-Oliveira, RM 2019, 'Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections', Frontiers in Microbiology, vol. 10, no. JULY. https://doi.org/10.3389/fmicb.2019.01647

TY - JOUR

T1 - Dual DNA barcoding for the molecular identification of the agents of invasive fungal infections

AU - Hoang, Minh Thuy Vi

AU - Irinyi, Laszlo

AU - Chen, Sharon C.A.

AU - Sorrell, Tania C.

AU - Meyer, Wieland

AU - Arabatzis, Michael

AU - Arthur, Ian

AU - Cano-Lira, Jose F.

AU - Cardinali, Gianluigi

AU - Castañón, Laura Rosio

AU - Chen, Wen

AU - Chindamporn, Ariya

AU - Colombo, Arnaldo L.

AU - Desnos-Ollivier, Marie

AU - De Beer, Wilhelm

AU - De Hoog, Sybren

AU - Fungal, Westerdijk

AU - Dromer, Françoise

AU - Garcia-Hermoso, Dea

AU - Gryzenhout, Marieka

AU - Guarro, Josep

AU - Halliday, Catriona

AU - Hendrickx, Marijke

AU - Huhndorf, Sabine

AU - Andre Levesque, C.

AU - Moretti, Maria Luiza

AU - De Medeiros Muniz, Mauro

AU - De Azevedo Melo, Analy Salles

AU - Nishikaku, Angela Satie

AU - Normand, Anne Cécile

AU - Pais, Célia

AU - Piarroux, Renaud

AU - Ranque, Stéphane

AU - Robbertse, Barbara

AU - Robert, Vincent

AU - Schoch, Conrad L.

AU - Seifert, Keith A.

AU - De Almeida Soares, Célia Maria

AU - Spouge, John L.

AU - Stubbe, Dirk

AU - Taylor, Maria Lucia

AU - Toriello, Conchita

AU - Velegraki, Aristea

AU - Yurayart, Chompoonek

AU - Zancopé-Oliveira, Rosely Maria

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Dual barcoding system

KW - Fungal DNA barcoding

KW - ISHAM Barcoding Database

KW - Identification

KW - Internal transcribed spacer region

KW - Invasive fungal diseases

KW - Translational elongation factor 1α

UR - https://www.mendeley.com/catalogue/96ae2304-6d2b-39fc-b5d6-878f36a14082/

U2 - 10.3389/fmicb.2019.01647

DO - 10.3389/fmicb.2019.01647

M3 - Article

SN - 1664-302X

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

IS - JULY

ER -

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

Abstract

Keywords

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