This paper introduces an approach to modeling and simulating the propagation of u-like infectious diseases over large, widely spread urban areas connected by transportation networks. We incorporate geographic location and a transportation model into our region-based, closed-world EpiGraph simulator to realistically model the movement of the virus between different geographic regions. The resulting simulator can assist in understanding how outbreaks propagate between far apart regions due to the movement of people outside their base location. This paper describes the MPI-based implementation of EpiGraph and its performance evaluation when simulating large-scale scenarios. We evaluate the simulator both on a distributed memory system and on a shared memory system.