Comparative Genomic Analysis of Pseudomonas aeruginosa Isolates from Community-Acquired and Hospital-Acquired Pneumonia

Feifei Yang,1,* Shukun Chai,2,* Li Yan,3,* Yukun He,1 Xinqian Ma,1 Lixiao Shen,2 Shuhui Gao,3 Yatao Guo,1,4 Zhao Zhang,1,4 Wentao Ni,1 Jing Bao,1 Zhancheng Gao1 1Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, People’s Republic of China; 2Department of Respiratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, People’s Republic of China; 3Department of Respiratory Medicine, Hebei General Hospital, Shijiazhuang, Hebei, People’s Republic of China; 4Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China*These authors contributed equally to this workCorrespondence: Jing Bao, Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, 100044, People’s Republic of China, Email [email protected] Zhancheng Gao, Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, 100044, People’s Republic of China, Email [email protected]: To characterize the genomic features of Pseudomonas aeruginosa isolates causing community-acquired pneumonia (CAP) and compare them with hospital-acquired pneumonia (HAP) genomes to identify setting-associated genetic determinants.Patients and Methods: Three CAP isolates collected in China underwent antimicrobial susceptibility testing and whole-genome sequencing. Comparative genomic analyses were performed against 84 complete HAP-associated genomes retrieved from NCBI RefSeq (accessed in December 2023), including core genome SNP phylogeny, profiling of antimicrobial resistance (AMR) determinants, virulence genes, and pangenome analysis to identify CAP-specific genes.Results: The three CAP cases presented with severe pneumonia (including septic shock), with one fatality; however, all CAP isolates remained susceptible to the most commonly used antipseudomonal agents. CAP genomes were 6.5– 7.1 Mb (GC 65.76– 66.41%) and contained 5908– 6633 predicted coding sequences. Core-SNP phylogeny showed clustering of the three CAP isolates. Compared with HAP genomes, CAP isolates harbored fewer acquired AMR genes and fewer resistance-associated mutations. Virulence profiling identified a subset of virulence genes absent from all CAP genomes (n = 40), largely annotated as immune modulation and including loci consistent with highly variable surface polysaccharide regions, together with several genes annotated to biofilm-related functions and effector delivery systems. Major type III secretion system effector profiles differed across CAP isolates (exoU in one isolate; exoS in two). Pangenome analysis identified 10,225 gene families, and 157 genes were specific to the CAP isolates, most encoding hypothetical proteins, with a subset related to lipid transport and metabolism, including fatty acid uptake and functions associated with β-oxidation. Given the limited number of CAP isolates, comparisons between groups are descriptive.Conclusion: CAP-associated P. aeruginosa showed a distinct comparative genomic profile with reduced AMR determinant burden and a distinct virulence gene repertoire despite severe clinical presentation. CAP-specific genes, including those linked to lipid metabolism, may contribute to niche adaptation and warrant functional validation.Keywords: Pseudomonas aeruginosa, community-acquired pneumonia, hospital-acquired pneumonia, comparative genomics, virulence, antimicrobial resistance