For bacteria, whole genome mapping will be developed, evaluated and standardised to enable real-time, high-resolution outbreak management. PREPARE will be linked with ongoing US and EU Public Health initiatives with the aim of mapping outbreak isolates from National Reference Centre or Public Health Institute collections who are partners in these initiatives. Mass spectrometry applications for the high-speed identification of bacterial pathogens will be developed as well as tests for defining their antibiotic resistance and virulence profiles. For viruses, next-generation sequencing technology is already being developed by the collaborating project EMPERIE, and the experiences there will be used to develop SOP’s for use of NGS for identification of viruses in diverse clinical samples, and for rapid deployment during outbreaks. In collaboration with the clinical studies of PREPARE, well defined selections of patients for which no aetiology could be identified, will be subjected to NGS to identify or rule out missed infections. Selection will be based on outcomes of comparative observational studies and focus on unusual presentations (age, severity, a.o., unusual clusters). If needed, findings will be used to optimise or develop diagnostic tests to be incorporated in rapid detection formats as described in Task 7.2, or for immediate deployment in case of epidemics as described in task 7.6.