Dotsch A

Goslee SC

Kulkarni MM

Mayer-Hamblett N

ABSTRACT
          
            The discovery of therapies that modulate
            Pseudomonas aeruginosa
            virulence or that can eradicate chronic
            P. aeruginosa
            lung infections associated with cystic fibrosis (CF) will be advanced by an improved understanding of
            P. aeruginosa
            behavior
            in vivo
            . We demonstrate the use of multiplexed Nanostring technology to monitor relative abundances of
            P. aeruginosa
            transcripts across clinical isolates, in serial samples, and for the purposes of comparing microbial physiology
            in vitro
            and
            in vivo
            . The expression of 75 transcripts encoded by genes implicated in CF lung disease was measured in a variety of
            P. aeruginosa
            strains as well as RNA serial sputum samples from four
            P. aeruginosa
            -colonized subjects with CF collected over 6 months. We present data on reproducibility, the results from different methods of normalization, and demonstrate high concordance between transcript relative abundance data obtained by Nanostring or transcriptome sequencing (RNA-Seq) analysis. Furthermore, we address considerations regarding sequence variation between strains during probe design. Analysis of
            P. aeruginosa
            grown
            in vitro
            identified transcripts that correlated with the different phenotypes commonly observed in CF clinical isolates.
            P. aeruginosa
            transcript profiles in RNA from CF sputum indicated alginate production
            in vivo
            , and transcripts involved in quorum-sensing regulation were less abundant in sputum than strains grown in the laboratory.
            P. aeruginosa
            gene expression patterns from sputum clustered closely together relative to patterns for laboratory-grown cultures; in contrast, laboratory-grown
            P. aeruginosa
            showed much greater transcriptional variation with only loose clustering of strains with different phenotypes. The clustering within and between subjects was surprising in light of differences in inhaled antibiotic and respiratory symptoms, suggesting that the pathways represented by these 75 transcripts are stable in chronic CF
            P. aeruginosa
            lung infections.
          </jats:p

Alex H. Gifford

Sven D. Willger

Emily L. Dolben

Lisa A. Moulton

Dana B. Dorman

Heather Bean

Jane E. Hill

Thomas H. Hampton

Alix Ashare

Deborah A. Hogan

Crossref

Infection and Immunity

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung

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