Answer
Assuming they were communicable, pathogens would reduce the carrying capacity by increasing the mortality rate proportionally with the population density.
Work Step by Step
Population density increases the spread of communicable diseases, as higher density populations can more easily spread the infection to more members of the population. Among humans we see this affect: the incidence of mass epidemics increases as large population centers arise and increase in density. With humans this is no longer necessarily something that will limit our population, but we are the exception.
If the pathogens are present in the environment but not able to spread from individual to individual, it may or may not affect carrying capacity depending on how it acted on the population and the affect of population density on the disease.