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We study the influence of heterogeneous mobility patterns in a population on the SIS epidemic model. In particular, we consider a patchy environment in which each patch comprises individuals belonging the different classes, e.g., individuals in different socio-economic strata. We model the mobility of individuals of each class across different patches through an associated Continuous Time Markov Chain (CTMC). The topology of these multiple CTMCs constitute the multi-layer network of mobility. At each time, individuals move in the multi-layer network of spatially-distributed patches according to their CTMC and subsequently interact with the local individuals in the patch according to an SIS epidemic model. We derive a deterministic continuum limit model describing these mobility-epidemic interactions. We establish the existence of a Disease-Free Equilibrium (DFE) and an Endemic Equilibrium (EE) under different parameter regimes and establish their (almost) global asymptotic stability using Lyapunov techniques. We derive simple sufficient conditions that highlight the influence of the multi-layer network on the stability of DFE. Finally, we numerically illustrate that the derived model provides a good approximation to the stochastic model with a finite population and also demonstrate the influence of the multi-layer network structure on the transient performance.