Tan, Shaoyuan2021-04-202021-04-202020-02https://hdl.handle.net/11299/219417University of Minnesota Ph.D. dissertation. 2020. Major: Veterinary Medicine. Advisors: Cheryl Dvorak, Mark Rutherford. 1 computer file (PDF); 156 pages.The swine industry is an indispensable part of the food production and agricultural system. However, infectious disease poses great threats to the industry. The current situation is that “old” infectious diseases are not totally under control and “new” pathogens keep emerging. In addition, via food chain and direct or indirect contact, some swine pathogens can infect humans and antimicrobial resistance arising from swine pathogens can also adversely impact public health. The threat of infectious disease to the swine population has been further magnified by globalization which increases the rate and breadth of disease transmission, thus having a more devastating impact. Fortunately, scientific advances have greatly bolstered our ability to develop effective disease control strategies. Sequencing technology has emerged as a powerful solution to deal with the challenging infectious disease situations we are facing today. The advantages of sequencing as a diagnostic tool are numerous. From our research, we confirmed that sequencing has improved the disease diagnostic resolution to the strain level, providing more precise and effective control strategies; it is able to generate additional genomic information for functional prediction of infectious agents, such as antimicrobial resistance profiling; and sequencing can facilitate a prompt response against emerging eventualities due to its ability to rapidly detect pathogens in a sample, including the novel or unexpected ones. Going forward, the more frequent use of sequencing in swine medicine can enhance our ability to predict and control the emergence and transmission of infectious disease within swine populations.enantibiotic resistancebioinformaticsemerging viral diseaseinfectious disease diagnosissequencingThesis or Dissertation