Influenza virus and Staphylococcus aureus super-infection disrupts spatially coordinated cellular immunity in the mouse lung

Influenza-associated bacterial super-infections in the lung lead to increased morbidity and mortality. Previous studies have investigated how preceding viral infection causes dysregulation of the innate and adaptive immune systems, leading to increased susceptibility of developing secondary bacterial pneumonia. However, these previous studies cannot account for the spatial context of immune cells in lung. In our study, we employ a spatial transcriptomics platform (10X Genomics Visium) to systematically characterize the coordination of immune cells during super-infection. We compare deconvoluted spatial transcriptomics data between super-infection and single influenza and methicillin-resistant Staphylococcus aureus infections. Consequently, we find that the recruitment of neutrophils and interstitial macrophages from lung parenchyma to the airways is inhibited in super-infection, likely impairing pathogen clearance. Additionally, by analyzing cell colocalization and signaling, we find that the interaction between CD4⁺ T cells, B cells, and dendritic cells is disrupted by secondary bacterial super-infection. These findings are confirmed by immunofluorescence staining. Our study constructs a spatial sequencing atlas of lung super-infection, highlighting how secondary bacterial challenge significantly impacts recruitment and signaling of immune cells. These findings provide insight into the aberrant inflammation in the super-infected lung and may aid development of therapeutics that target key immune cell recruitment pathways.