Identification of drug targets in pan-drug resistant Acinetobacter baumannii via whole genome sequencing and subtractive genomics

In this study, we report, to the best of our knowledge, the first complete genome sequence of a pan drug resistant (PDR) Acinetobacter baumannii strain (JRCGR-AK-AB-01) from Karachi, Pakistan. Strain JRCGR-AK-AB-01 exhibited a pan drug resistant phenotype, showing susceptibility only to polymyxin B and intermediate susceptibility to colistin. Hybrid genome sequencing using MinION long-reads and DNBSEQ short-reads revealed that the genome size of strain JRCGR-AK-AB-01 is 4.03 Mb. We identified that JRCGR-AK-AB-01 is closely related to other A. baumannii strains based on Average Amino Acid Identity (AAI), Genome-to-Genome Distance Calculator (GGDC), and Average Nucleotide Identity (ANI) analyses. Furthermore, pan-genome analysis revealed an open pan-genome, indicating frequent gene exchange. Subsequently, a subtractive genomics approach was employed to identify potential drug targets within the core genes that are essential, druggable, and non-homologous to both human proteins and gut microbiota. Finally, the selected genes were screened against the JRCGR-AK-AB-01 proteome to eliminate redundancies. Among these, NADP-dependent isocitrate dehydrogenase (IDH) was used for downstream analysis. Its structure was predicted via homology modeling and validated using different bioinformatics tools. Molecular docking and molecular dynamics (MD) simulations revealed that neomycin and paromomycin were the potent drugs against Acinetobacter spp. In vitro studies confirmed that neomycin (2.25 mg/mL) exhibited antimicrobial activity against the PDR strain of A. baumannii. Overall, this study defines genomic features and identifies potential therapeutic targets in PDR A. baumannii, thereby providing a foundation for future experimental validation and novel treatment strategies.