Delftia tsuruhatensis is an opportunistic pathogen, that causes human infection in immunocompromised individuals. The organism was found to be infectious in the respiratory tract and urinary tract infections. Isolation of D. tshuruhatensis showed resistance to common antibiotics, resulting in an alarming signal from the pathogen. Importantly, the D. tshuruhatensis strain was found to have the property of having IMP-1 Metallo-β-Lactamase, which could hydrolyze β-lactam antibiotics. To combat the challenge of antibiotic resistance, novel drug targets can be effective. For suggesting the novel drug targets, the entire proteome of D. tshuruhatensis strain TR1180 was subjected to subtractive genomic analysis using a variety of bioinformatic tools and servers. To identify human homologue proteins of the pathogen and proteins involved in common metabolic pathways between the pathogen and host, various bioinformatics tools and web servers were used. Only 62 proteins were found to be linked to pathogen-specific pathways; these proteins were then further screened to single out membrane-antigenic proteins that could be targeted by medications or vaccines. The novel therapeutic targets with the highest level of antigenicity were discovered to be ‘Nitrate transporter’ and ‘Phospho-N-acetylmuramoyl-pentapeptide-transferase’.