Cystic fibrosis rapid response: Translating multi-omics data into clinically relevant information

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

Research output: Contribution to journalArticlepeer-review

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Pulmonary exacerbations are the leading cause of death in cystic fibro-sis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenom-ics, 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 compli-cated disease dynamics and provide clinicians with alternative treatments to im-prove 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.

Original languageEnglish
Article numbere00431-19
Number of pages15
Issue number2
Publication statusPublished - 1 Mar 2019
Externally publishedYes

Bibliographical note

Copyright © 2019 Cobián Güemes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.


  • Clinical metagenomics
  • Cystic fibrosis
  • Metabolomics
  • Metatranscriptome
  • Shiga toxins


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