Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information

ABSTRACT Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidl...

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Autores principales:	Ana Georgina Cobián Güemes, Yan Wei Lim, Robert A. Quinn, Douglas J. Conrad, Sean Benler, Heather Maughan, Rob Edwards, Thomas Brettin, Vito Adrian Cantú, Daniel Cuevas, Rohaum Hamidi, Pieter Dorrestein, Forest Rohwer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Shiga toxins clinical metagenomics cystic fibrosis metabolomics metatranscriptome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a2d51f7ea3ee43cc9a4512176910b72f
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spelling	oai:doaj.org-article:a2d51f7ea3ee43cc9a4512176910b72f2021-11-15T15:55:25ZCystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information10.1128/mBio.00431-192150-7511https://doaj.org/article/a2d51f7ea3ee43cc9a4512176910b72f2019-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00431-19https://doaj.org/toc/2150-7511ABSTRACT Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient’s lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF. IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli. The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.Ana Georgina Cobián GüemesYan Wei LimRobert A. QuinnDouglas J. ConradSean BenlerHeather MaughanRob EdwardsThomas BrettinVito Adrian CantúDaniel CuevasRohaum HamidiPieter DorresteinForest RohwerAmerican Society for MicrobiologyarticleShiga toxinsclinical metagenomicscystic fibrosismetabolomicsmetatranscriptomeMicrobiologyQR1-502ENmBio, Vol 10, Iss 2 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Shiga toxins clinical metagenomics cystic fibrosis metabolomics metatranscriptome Microbiology QR1-502
spellingShingle	Shiga toxins clinical metagenomics cystic fibrosis metabolomics metatranscriptome Microbiology QR1-502 Ana Georgina Cobián Güemes Yan Wei Lim Robert A. Quinn Douglas J. Conrad Sean Benler Heather Maughan Rob Edwards Thomas Brettin Vito Adrian Cantú Daniel Cuevas Rohaum Hamidi Pieter Dorrestein Forest Rohwer Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
description	ABSTRACT Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient’s lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF. IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient’s microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli. The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.
format	article
author	Ana Georgina Cobián Güemes Yan Wei Lim Robert A. Quinn Douglas J. Conrad Sean Benler Heather Maughan Rob Edwards Thomas Brettin Vito Adrian Cantú Daniel Cuevas Rohaum Hamidi Pieter Dorrestein Forest Rohwer
author_facet	Ana Georgina Cobián Güemes Yan Wei Lim Robert A. Quinn Douglas J. Conrad Sean Benler Heather Maughan Rob Edwards Thomas Brettin Vito Adrian Cantú Daniel Cuevas Rohaum Hamidi Pieter Dorrestein Forest Rohwer
author_sort	Ana Georgina Cobián Güemes
title	Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
title_short	Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
title_full	Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
title_fullStr	Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
title_full_unstemmed	Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information
title_sort	cystic fibrosis rapid response: translating multi-omics data into clinically relevant information
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/a2d51f7ea3ee43cc9a4512176910b72f
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Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information

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