The pig industry has evolved extremely fast during the last decades. The exponential increase in the number of animals combined with their worldwide transport and the globalization of feed components favors a continuous fast spread of infectious agents throughout the world. Major gaps in their control are difficulties to (1) recognize diseases at an early stage, (2) swiftly identify pathogens and pathogen complexes, and (3) convince farmers on the importance of an efficient biosecurity. Novel technologies will now be used to address these issues. (1) Real-time detection of clinical signs using sensors recording animal physiological and environmental conditions (Healthy Climate Monitor). (2) Use of a new sampler developed by Ghent University allowing on-site purification of material from live and deceased animal. Direct nanopore sequencing and data analysis through a novel diagnostic software platform allow rapid virus and bacteria identification, without the need of any prior pathogen knowledge. (3) A risk-based biosecurity scoring system (Biocheck.UGent) to evaluate the quality of the on-farm biosecurity. These technologies will be first applied to farms without overt clinical signs but with low productivity. This will allow recommendations to improve the biosecurity level. Subclinical bacteria and virus circulation will come to light. Secondly, the same technologies will be used on farms with clinical outbreaks. The pathogens will be identified together with negative environmental and biosecurity factors. This will allow to develop pathogen-specific treatments and prevention together with adaptation of the environment and biosecurity. Newly identified viral isolates will be used in experimental infections to determine their clinical and pathological outcome. Finally, a spatio-temporal pathogen tracking system for veterinary medicine will be developed for farmers, veterinarians, decision makers and pharmaceutical companies as a tool for surveilling and combating emerging endemic and epidemic viral diseases.