The rapid advances in sequencing and computational technologies accompanied by a drastic reduction of sequencing costs, have revolutionized microbial genomics and provided an unprecedented insight into microbial evolution, diversity, and host–pathogen interaction. Moreover, genomic technologies demonstrated great potential and suitability for clinical diagnostics or the real-time detection and surveillance of epidemics. The overall goal of the PREPMedVet is to set up a portable diagnostic sequencing platform (iSeq100, Illumina) capable to deliver in a clinically relevant turnaround time critical information in the context of an outbreak. The consortium has aimed to develop a standard wet-lab protocol which could be applied on-site using portable next-generation sequencing platforms and user-friendly sequence analysis software’s capable to deliver valuable insight into epidemic transmission patterns, pathogen genomics, evolution and the possible source of origin. The identification of pathogens will be flanked by production and validation of easy-to-use detection assays that can be stockpiled, transported, and delivered to the end users for timely and comprehensive reaction on outbreak scenarios.