Unlike the traditional approach of examining the host or pathogen separately, a systems-level approach, which considers the pathogen and host together as a whole, is essential to elucidate the mechanisms which contribute to the initiation, progression, and persistence of bacterial and viral infections. Furthermore, understanding infection-induced metabolic, lipidomics and proteomic changes can reveal pathways required for pathogenesis, identify targets for the prevention of host colonization, and reveal the metabolic cross-talk that occurs at the host-pathogen interface. Our research includes characterizing the large array of altered biomolecules using mass-spectrometry based proteomic studies and profile metabolites in infected and drug treated tissues using FTICR-imaging mass spectrometry. The data generated is used in computational network constructions to predict key pheotype of pathogenesis and identify novel therapeutic targets.