High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation.

Mitchell, AB; Li, C-X; Oliver, BGG; Holmes, EC; Glanville, AR

High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation.

Mitchell, AB Li, C-X Oliver, BGG Holmes, EC Glanville, AR

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Publisher:: Ovid Technologies (Wolters Kluwer Health)
Publication Type:: Journal Article
Citation:: Transplantation, 2021, 105, (12), pp. 2546-2553
Issue Date:: 2021-12-01

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Field	Value	Language
dc.contributor.author	Mitchell, AB
dc.contributor.author	Li, C-X
dc.contributor.author	Oliver, BGG
dc.contributor.author	Holmes, EC
dc.contributor.author	Glanville, AR
dc.date.accessioned	2022-01-14T03:13:08Z
dc.date.available	2022-01-14T03:13:08Z
dc.date.issued	2021-12-01
dc.identifier.citation	Transplantation, 2021, 105, (12), pp. 2546-2553
dc.identifier.issn	0041-1337
dc.identifier.issn	1534-6080
dc.identifier.uri	http://hdl.handle.net/10453/153104
dc.description.abstract	BACKGROUND: Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome. METHODS: We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited. RESULTS: mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients. CONCLUSIONS: Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.
dc.format	Print
dc.language	eng
dc.publisher	Ovid Technologies (Wolters Kluwer Health)
dc.relation.ispartof	Transplantation
dc.relation.isbasedon	10.1097/TP.0000000000003713
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	11 Medical and Health Sciences
dc.subject.classification	Surgery
dc.title	High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation.
dc.type	Journal Article
utslib.citation.volume	105
utslib.location.activity	United States
utslib.for	11 Medical and Health Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Centre for Health Technologies (CHT)
utslib.copyright.status	closed_access	*
dc.date.updated	2022-01-14T03:13:07Z
pubs.issue	12
pubs.publication-status	Published
pubs.volume	105
utslib.citation.issue	12

Abstract:

BACKGROUND: Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome. METHODS: We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited. RESULTS: mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients. CONCLUSIONS: Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.

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http://hdl.handle.net/10453/153104