Multidrug-resistant (MDR) and virulent pathogenic strains of Pseudomonas aeruginosa (Pa) are among the most dangerous pathogens in healthcare-associated infections. 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 carbapenemresistant 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, pili, 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 severalmultidrug resistance genes: aacA27, β-lactamase OXA-2 (bla OXA-2 ), qacΔE, sul1, and GNAT-N, in the chronic strain, CMC-097. This comparative analysis revealed several important differences in gene expression between the two strains that may lead to identification of targets for better therapy and hospital management.