Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, an...
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Autor*in:	Zackary Salem-Bango [verfasserIn] Travis K Price [verfasserIn] June L Chan [verfasserIn] Sukantha Chandrasekaran [verfasserIn] Omai B Garner [verfasserIn] Shangxin Yang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	fungal species identification next-generation sequencing whole-genome sequencing fungal infections ITS 28S rRNA

Übergeordnetes Werk:	In: Journal of Fungi - MDPI AG, 2015, 9(2023), 2, p 183
Übergeordnetes Werk:	volume:9 ; year:2023 ; number:2, p 183

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/jof9020183

Katalog-ID:	DOAJ080239870

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callnumber-first	Q - Science
author	Zackary Salem-Bango
spellingShingle	Zackary Salem-Bango misc QH301-705.5 misc fungal species identification misc next-generation sequencing misc whole-genome sequencing misc fungal infections misc ITS misc 28S rRNA misc Biology (General) Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization
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topic_title	QH301-705.5 Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization fungal species identification next-generation sequencing whole-genome sequencing fungal infections ITS 28S rRNA
topic	misc QH301-705.5 misc fungal species identification misc next-generation sequencing misc whole-genome sequencing misc fungal infections misc ITS misc 28S rRNA misc Biology (General)
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title	Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization
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title_full	Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization
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title_sort	fungal whole-genome sequencing for species identification: from test development to clinical utilization
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title_auth	Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization
abstract	Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and <i<Aspergillus</i< genus (using the beta-tubulin gene and <i<k-mer</i< tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.
abstractGer	Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and <i<Aspergillus</i< genus (using the beta-tubulin gene and <i<k-mer</i< tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.
abstract_unstemmed	Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and <i<Aspergillus</i< genus (using the beta-tubulin gene and <i<k-mer</i< tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.
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