After half a century of antibiotic use, re-emerging and new infectious diseases, partially caused by the rise of antimicrobial resistance, have become a major public health concern. Antibiotic resistances lead to escalating healthcare costs, increased morbidity and mortality and the emergence of potentially untreatable conditions. The DebugIT project, a consortium of leading European clinical, academic and industrial partners, aims at developing an IT-framework to allow healthcare systems to better address these emergent problems and improve their management.