Sean Nair's research is focused in two main areas:
(i) The interactions of bacteria with host cells in health and disease where his primary focus is on the mechanisms by which staphylococci, and other hospital-acquired pathogens such as enterococci cause disease.
(ii) The development of novel antimicrobial strategies to combat infections. These strategies currently include the use of antisense and aptamer technologies, development of new light-activated antimicrobial agents and the identification of bacterial genes coding for potential novel therapeutic targets.