Comparative and subtractive genomics reveals novel therapeutic targets in cystic fibrosis-associated multidrug-resistant Pandoraea sputorum.

Despite increasing clinical reports of its emergence and multidrug resistance, particularly in cystic fibrosis (CF) patients, comprehensive genomic insights and effective therapeutic strategies targeting P. sputorum remain scarce. This study aimed to elucidate the evolutionary relationships and genomic characteristics of P. sputorum and to identify potential therapeutic targets and repurposable drugs via integrated computational approaches. Phylogenetic relationships were reconstructed via 16S rRNA gene sequences retrieved from the NCBI GenBank database, followed by comprehensive whole-genome-based comparative genomic analyses. Functional pathway and resistance gene profiling were conducted to characterize virulence and antimicrobial resistance traits. A subtractive genomics pipeline integrating Orthofinder, the Database of Essential Genes, BLASTp against the human proteome, and KEGG pathway analysis was applied to identify essential, non-host homologous drug targets. Structural modeling, binding pocket characterization, molecular docking, and protein-ligand interaction analyses were employed to screen and evaluate repurposable drug candidates. The results demonstrated that P. sputorum is closely related to Burkholderia species and shares a conserved genomic backbone while exhibiting notable genomic diversification. Functional profiling revealed shared antimicrobial resistance mechanisms, including efflux pumps and β-lactamases. Subtractive genomics prioritized three conserved cytoplasmic targets, LpxC, MurA, and DnaE. Structure-based molecular docking identified ten FDA-approved drugs with strong and stable binding affinities toward these targets. Notably, lumacaftor is a drug currently used in cystic fibrosis therapy. This study provides a comprehensive genome-guided framework for understanding P. sputorum and identifying therapeutic opportunities. The identified drug targets and repurposed candidates offer promising avenues for combating multidrug-resistant P. sputorum infections, particularly in CF and immunocompromised patients.