Comparative transcriptomic analysis of Pseudomonas aeruginosa isolates from ICU patients with acute and chronic pneumonia

In this study, a comparative analysis was performed on two clinical Pa strains from pneumonia patients, 1) an acute strain (CMC-115) and 2) a chronic multidrug- and carbapenem-resistant strain (CMC-097), with distinct phenotypic and genetic characteristics. A transcriptome analysis using both the Pseudomonas DNA GeneChip microarray and Illumina RNA-Seq technologies was carried out for both strains at early-stationary growth phase in laboratory culture. The comparative transcriptomic analysis identified 134 genes differentially expressed ≥4.0-fold by both technologies between the two strains, which included virulence genes such as flagellar, pyoverdine, and phenazine genes, that were higher in the acute strain, CMC-115, and type 3 secretory system (T3SS) and pyochelin biosynthesis genes, that were higher in the chronic strain, CMC-097. In particular, the DNA microarrays suggested and the RNA-Seq analysis confirms the type 3 secretory system genes were completely missing from the acute strain, CMC-115. The combined analysis using the RNA-Seq and DNA microarray methods also identified important genes that were either missing or highly divergent from the Reference PAO1 genome used for the DNA microarray design. For example, the RNA-Seq data identified an operon containing several multidrug resistance genes: aacA27, beta-lactamase (blaOXA-2), qacΔE, sul1, and GNAT-N, in the chronic strain, CMC-097. This GEO DataSet contains the Illumina RNA-Seq analysis carried out for 3 biological replicates of both strains at early-stationary growth phase in laboratory culture.