Long-read sequencing in fungal identification
Minh Thuy Vi Hoang A B , Laszlo Irinyi A B C and Wieland Meyer A B C D E *A Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006, Australia.
B Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia.
C Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia.
D Westmead Hospital (Research and Education Network), Westmead, NSW 2145, Australia.
E Curtin Medical School, Curtin University, Perth, WA 6102, Australia.
Minh Thuy Vi Hoang is a PhD student at the University of Sydney at the Sydney Medical School. Her doctoral work explores the application of long-read sequencers to the diagnosis of fungal diseases. Prior, she received a Bachelor of Medical Science (First Class Honours) in Microbiology at the University of Sydney. |
Dr Laszlo Irinyi is a Postdoctoral Fellow at Westmead Institute for Medical Research, Westmead, NSW, Australia and his research focuses on the identification and molecular taxonomy of human and animal pathogenic fungi. Currently his focus is on the adaptation of new generation sequencing technologies in routine diagnostics for fungal identification. |
Professor Wieland Meyer is a Molecular Medical Mycologist and academic at the Faculty of Medicine and Health, Sydney Medical School; The University of Sydney, Associate Dean of Curtin Medical School, Curtin University, and the Fundação Oswaldo Cruz (FIOCRUZ) in Rio de Janeiro, Brazil, heading the MMRL within the CIDM, Westmead Institute for Medical Research, with a PhD in fungal genetics from the Humboldt University of Berlin, Germany. His research focuses on phylogeny, molecular identification, population genetics, molecular epidemiology, and virulence mechanisms of human and animal pathogenic fungi. He is the Convener of the Mycology Interest Group of ASM, and the President of the International Mycological Association (IMA). |
Microbiology Australia 43(1) 14-18 https://doi.org/10.1071/MA22006
Submitted: 23 December 2021 Accepted: 11 February 2022 Published: 8 April 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing on behalf of the ASM. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Long-read sequencing is currently supported by sequencing platforms from Pacific Biosciences and Oxford Nanopore Technologies, both of which generate ultra-long reads. Metabarcoding and metagenomics are the two approaches used when implementing sequencing. Metabarcoding involves the amplification and sequencing of selected nucleic acid regions, while in a metagenomic approach extracted nucleic acids are sequenced directly without prior amplification. Both approaches have associated advantages and disadvantages, which, in combination with long-read sequencing, provide a promising new approach for fungal identification and diagnosis of mycoses, on which we will reflect in this short review.
Keywords: diagnostics, DNA barcoding, fungal identification, long-read sequencing, metabarcoding, metagenomics, mycoses, next generation sequencing.
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