Many pathogens in the environment can be transmitted to human populations and cause outbreaks and epidemics. Transmission is a multifactorial process influenced by the physiology of the pathogen as it exits its initial host, the mechanisms it uses for surviving outside the host, the physiology of the pathogen as it enters the next susceptible host and its ability to establish a successful infection. Few studies so far have focused on the processes responsible for modulating microbial survival in non-host environments and the transmission dynamics between infected and susceptible hosts, as well as the interplay between hosts. A better understanding of these mechanisms is thus necessary for predicting and preventing future outbreaks.