Alveolar macrophages (AMs) serves as a frontline innate barrier against pulmonary bacterial invasion. The AM pool comprises tissue-resident AMs (TR-AMs) and monocyte-derived AMs (Mo-AMs); yet how vaccination remodels the mixed AM pool for long-term antimicrobial defense against multidrug-resistant bacteria remains poorly understood. In this work, we applied intranasal inactivated whole-cell (IWC) vaccination against Acinetobacter baumannii and systematically dissected AM population dynamics at cellular and molecular levels. Vaccination reshaped the AM pool by recruiting CD11B+CD13+ Mo-AMs that gradually acquire a TR-AMs-like phenotype and training TR-AMs via sustained transcriptional adaptations. Functionally, the IWC-remodeled AM pool exhibited enhanced antigen presentation, TNF-α secretion, and phagocytosis, accompanied by metabolic rewiring, thereby conferring durable protection against A. baumannii infection. ATAC-seq revealed immune-related chromatin remodeling and enrichment of transcription factors, including ETS, IRF, and bZIP family members. Similar AM pool remodeling was observed following immunization with IWC vaccines against Pseudomonas aeruginosa and Klebsiella pneumoniae, suggesting parallel innate responses across multiple common respiratory bacterial vaccines. Collectively, our study delineates the single-cell transcriptional and epigenetic landscapes of vaccine-remodeled AM subsets, providing mechanistic insights to guide the development of AM-targeted prophylactic vaccines against multidrug-resistant A. baumannii.
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