Immune-adaptive pathogen variation reveals targetable mediators of gram-positive bacterial killing in macrophages

Host-directed therapies for bacterial infections can provide an adjunct or alternative to conventional antimicrobials, mitigating the impact of antimicrobial resistance. However, therapeutically targetable mediators of innate immune bacterial killing remain elusive. We hypothesized that immune-adaptive pathogen evolution could provide an informative perspective on this problem. We examined the interaction of a genetically diverging hypervirulent Streptococcus pneumoniae (pneumococcus) serotype with macrophages, identifying closely phylogenetically related isolates with differential susceptibility to intracellular killing. We reasoned that macrophage genes relatively suppressed during pathogen escape from killing were likely to encode mediators normally promoting bacterial killing. This led to the validation of ACOD1 and its product itaconate, NAMPT, and P2RX7 as host defense factors against pneumococci and related gram-positive pathogens. Last, we repurposed the antihistamine clemastine to augment phagolysosomal bacterial killing, via P2RX7, as a candidate host-directed therapy against pneumococci and vancomycin-resistant Enterococcus faecium. Overall, we show that pathogen-centric host screening can aid identification of microbicidal responses as targets for host-directed therapies.