ABSTRACTPseudomonas aeruginosais an opportunistic pathogen that causes nosocomial pneumonia and infects patients with cystic fibrosis.P. aeruginosalung infections are difficult to treat due to bacterial resistance to antibiotics, and strains with multidrug resistance are becoming more prevalent. Here, we examined the use of a small host defense peptide, innate defense regulator 1002 (IDR-1002), in an acuteP. aeruginosalung infectionin vivo. IDR-1002 significantly reduced the bacterial burden in bronchoalveolar lavage fluid (BALF), as well as MCP-1 in BALF and serum, KC in serum, and interleukin 6 (IL-6) in BALF. Transcriptome sequencing (RNA-Seq) was conducted on lungs and whole blood, and the effects ofP. aeruginosa, IDR-1002, and the combination ofP. aeruginosaand IDR-1002 were evaluated. Differential gene expression analysis showed thatP. aeruginosaincreased multiple inflammatory and innate immune pathways, as well as affected hemostasis, matrix metalloproteinases, collagen biosynthesis, and various metabolism pathways in the lungs and/or blood. Infected mice treated with IDR-1002 had significant changes in gene expression compared to untreated infected mice, with fewer differentially expressed genes associated with the inflammatory and innate immune responses to microbial infection, and treatment also affected morphogenesis, certain metabolic pathways, and lymphocyte activation. Overall, these results showed that IDR-1002 was effective in treatingP. aeruginosaacute lung infections and associated inflammation.