His research has focused on the epidemiology and genomic epidemiology of important pathogens, including Streptococcus pneumoniae, group B Streptococcus, Neisseria meningitidis, methicillin-resistant Staphylococcus aureus, Clostridium difficile, SARS-CoV-2 and other respiratory viruses. A major focus of his research is methods for enhanced detection of hospital-acquired transmission of bacterial and viral pathogens using whole genomic sequencing surveillance and data mining of the electronic health record. Dr. Harrison is also the Program Director of three NIH training grants: 1) A T32 program on antimicrobial resistance 2) a D43 international training grant on HIV infection in Mozambique, and 3) a D43 international training grant on public health genomics in South Africa.