Breaking the population barrier by single cell analysis: one host against one pathogen

Highlights • Heterogeneity in host–pathogen interactions has long been recognized but remains poorly characterized. • Single cell interactions likely determine infection outcome. • The recent explosion in single cell methods is poised to lead to a resurgence in the field of host–pathogen interactions. • We review here the major gaps of in vivo infection that can be addressed by single cell RNA-seq methods.