Host Prior Exposure Augments Gene Expression Heterogeneity of Both Host and Pathogen During In Vivo Infection

Variability in acquired protection, whether from prior infection or vaccination, helps drive inter-individual level variation in disease traits. It remains unclear, however, whether this extends to the within-host regulatory environment and what the consequences are for reinfecting pathogens. Here, we asked whether prior pathogen exposure of hosts induces gene expression heterogeneity in host and/or pathogen during infection. We quantified gene expression in vivo following a high-dose challenge of house finches (Haemorhous mexicanus) previously given controlled, varied exposures to a bacterial pathogen (Mycoplasma gallisepticum). To measure gene expression heterogeneity, we collected transcriptomic data from two host tissues (conjunctiva and spleen), and simultaneously, from pathogen at the primary site of infection (conjunctiva). In conjunctiva, but not spleen, prior pathogen exposure induced significant heterogeneity in host gene expression relative to pathogen-naïve hosts, even when accounting for effects of sex. Hosts given a lower versus higher prior exposure dose showed the greatest within-group heterogeneity in expression during re-challenge. Functional enrichment analyses for significantly variable host genes indicated an over-representation of terms involved in the immune response among birds with prior exposure. Infecting pathogen from the conjunctiva followed similar heterogeneity patterns, with more heterogeneous expression among pathogens infecting previously exposed hosts than those infecting naïve hosts. While the mechanisms underlying these patterns remain unresolved, our results indicate that prior exposure induces a within-host environment that promotes heterogeneous gene expression across both hosts and pathogens. This suggests that gene expression variation in host and pathogen should be considered alongside sequence variation to understand the coevolutionary dynamics of infectious diseases.