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The discovery of therapies that modulatePseudomonas aeruginosa virulence or that can eradicate chronicP. aeruginosa lung infections associated with cystic fibrosis (CF) will be advanced by an improved understanding ofP. aeruginosa behaviorin vivo . We demonstrate the use of multiplexed Nanostring technology to monitor relative abundances ofP. aeruginosa transcripts across clinical isolates, in serial samples, and for the purposes of comparing microbial physiologyin vitro andin vivo . The expression of 75 transcripts encoded by genes implicated in CF lung disease was measured in a variety ofP. aeruginosa strains as well as RNA serial sputum samples from fourP. 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 ofP. aeruginosa grownin 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 productionin 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-grownP. 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 CFP. aeruginosa lung infections.

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