Even in a lab-grown monoculture, bacterial gene expression can be highly heterogeneous. Many mammalian cell types also exhibit considerable variability in gene expression states. Thus, the interactions between individual pathogenic bacteria and host cells tend to lead to highly variable outcomes. The outcome of the resulting infection on a cellular level may range from complete clearance of infection to persistent survival of intracellular bacteria. We aim to explain and predict the outcomes of intracellular infection at the level of individual interacting cells based on the simultaneous high-resolution measurements of both host and pathogen gene expression states. To this end, we develop and employ custom dual host-pathogen single-cell sequencing technologies.