Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii
The Gram-negative pathogen, Acinetobacter baumannii, poses a serious threat to human health by causing antibiotic-resistant nosocomial infections. Despite this, our understanding of fundamental A. baumannii biology remains limited, as many essential genes have not been experimentally characterized. Further, essential genes are critical for bacterial survival and, thus, represent promising targets for drug discovery. Here, we systematically probe the function of essential genes by screening a CRISPR interference knockdown library against a diverse panel of chemical inhibitors, including antibiotics. We find that most essential genes show chemical-gene interactions, allowing insights into both inhibitor and gene function. For instance, knockdown of lipooligosaccharide transport genes increased sensitivity to a broad swath of chemicals due to cell envelope hyper-permeability that depended on lipooligosaccharide production. Using patterns of phenotypes in our chemical-gene interaction dataset, we constructed an essential gene network linking poorly understood genes to well-characterized genes in cell division and other processes. Finally, our phenotype-structure analysis identified structurally related antibiotics with distinct cellular impacts and suggested potential targets for underexplored inhibitors. This study advances our understanding of essential gene and inhibitor function, providing a valuable resource for mechanistic studies, therapeutic strategies, and future key targets for antibiotic development.