biostudies-literatureLiu TNIAID NIH HHSNHLBI NIH HHSU.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)NIH HHS1837https://www.ebi.ac.uk/biostudies/studies/S-EPMC12749005biostudies-literatureUnknown8(1)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 inCommunications biologyInfluenza virus and Staphylococcus aureus super-infection disrupts spatially coordinated cellular immunity in the mouse lung.PMC12749005P01 AI106684HL167449S10 OD028483T32 AI060525R01 HL107380R01 HL167449AI060525AI106684HL107380Rangel-Garcia ARangel-Moreno JAlcorn JFZhao CMiller LMDresden BPChen WGarcia-Hernandez MLLiu TPillai YfalseInfluenza 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 in2025-01-01T00:00:00Z2025 Nov2026-06-06T09:45:51.638Z2026-05-28T03:12:25.186ZS-EPMC127490054127670710.1038/s42003-025-09268-1