Knowledge of the changes in the immune microenvironment during pulmonary bacterial acute and chronic infections is limited. The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. Here, we describe a single immune cell atlas of mouse lungs after acute and chronic Pseudomonas aeruginosa infection using single‐cell transcriptomics, multiplex immunohistochemistry, and flow cytometry. Our single‐cell transcriptomic analysis revealed large‐scale comprehensive changes in immune cell composition and high variation in cell–cell interactions after acute and chronic P. aeruginosa infection. Bacterial infection reprograms the genetic architecture of immune cell populations. We identified specific immune cell types, including Cxcl2+ B cells and interstitial macrophages, in response to acute and chronic infection, such as their proportions, distribution, and functional status. Importantly, the patterns of immune cell response are drastically different between acute and chronic infection models. The distinct molecular signatures highlight the importance of the highly dynamic cell–cell interaction process in different pathological conditions, which has not been completely revealed previously. These findings provide a comprehensive and unbiased immune cellular landscape for respiratory pathogenesis in mice, enabling further understanding of immunologic mechanisms in infection and inflammatory diseases.

The earliest single-cell transcription technique can only detect a handful of genes in a single cell with relatively low throughput. 1 Historically, scRNA-seq was applied when limited by the number of biological materials such as cells from early embryonic development. 2 It was not until 2009 that the single-cell transcriptome was combined with high-throughput sequencing, which allowed for improved throughput of gene detection and more detected transcripts than chips. 3 The impact of scRNA-seq has grown rapidly since 'single-cell sequencing' was selected as the method of 2013, mainly because of its high throughput of droplet or combinatorial indexing approaches and its wide use of advanced equipment, reagents and analysis tools. 4 In recent years, scRNA-seq has developed remarkably in the immune systems with the identification of transcriptionally distinct cell types unknown before, which has helped biologists obtain deeper insights into their research areas. [5][6][7][8] There are many distinct cell lineages localizing in primary and secondary lymphoid organs in immune systems. They also exist in tissues throughout the body and have dynamic abilities to migrate through the peripheral blood. 9 Recent advances in scRNA-seq and sophisticated bioinformatic methods have renewed our eyes on understanding immunology, which may help us reveal novel therapeutic targets from individual cells masked previously by bulk analysis.