This work aims at predicting continuum breakdown in high-speed, chemically reacting wake flows using breakdown parameters obtained from the generalized Champan-Enskog (GCE) theory. Previous efforts have addressed the mathematical development of these mechanism driven breakdown parameters and their utility in predicting continuum breakdown in high Mach number compressing flows. Here we present a specieswise perturbation parameter, based on the 2-norm in Hilbert space of the first-order GCE perturbation, which can be used to assess the extent to which the underlying equilibrium Maxwell-Boltzmann (MB) distribution of a given species has been perturbed. This parameter is derived for the one-, two-, and three-temperature models, and is applicable to multicomponent, chemically reacting flowfields. All transport mechanisms that can lead to distortion of the specieswise equilibrium MB distribution function-translational, rotational and vibrational heat fluxes, mass and thermal diffusion fluxes, and stress tensor components including bulk viscosity and relaxation pressure terms-are simultaneously incorporated into this perturbation parameter that can be computed for each species. This parameter and the mechanism-based GCE breakdown parameters are used to assess continuum breakdown in the forebody and wake region of a cylinder subjected to hypersonic flow. The influence of altitude, freestream velocity, and cylinder surface reactions on continuum breakdown is analyzed. Regions of continuum breakdown are observed in the shock, boundary layer, as well as in the wake. Most notably, the surface chemistry at the cylinder wall forebody can lead to the formation of breakdown regions in the wake that are detached from the cylinder surface.