Single-cell multi-omics reveals distinct immune suppression in refractory Mycoplasma pneumoniae pneumonia

Mycoplasma pneumoniae infection commonly manifests as atypical pneumonia in children and generally resolves without complications. However, some pediatric patients experience severe, prolonged disease, which sometimes results in fatal outcomes. The underlying immune responses associated with refractory Mycoplasma pneumoniae pneumonia (RMPP) remain poorly understood. Therefore, in this study, we conducted single-cell RNA-sequencing, B cell receptor/T cell receptor sequencing, and cytometry by time of flight analysis on peripheral blood mononuclear cells and bronchoalveolar lavage fluid samples from patients with RMPP, self-resolving M. pneumoniae pneumonia, and healthy controls. Our investigation revealed significant dysregulation in the peripheral circulatory immune system of patients with RMPP, potentially driven by chronic inflammation and the transition of monocytic myeloid-derived suppressor cells (MDSCs). Specifically, we observed pronounced interferon response dysregulation across innate immune cells. Moreover, the antigen presentation functions in antigen-presenting cells, particularly dendritic cells, were impaired. Remarkably, monocytes in individuals with RMPP showed considerable changes with increased expression of genes, such as SOCS3, S100A8, S100A9, and the C1q family, thus suggesting an MDSC-like transition. This phenotypic shift was exacerbated within the lung microenvironment, where CD14 + CD16 + monocytes infiltrated the tissue and differentiated into APOE + /M2 macrophages, which was triggered by CSF1, ANXA1, and TGFB1. This transition in macrophage phenotype and antigen-presenting capabilities notably hindered the activation of the adaptive immune response. Our findings reveal that patients with RMPP exhibit functional dysregulation of innate immune cells and impaired communication between the innate and adaptive immune systems. In summary, our study delineated immune dysregulation in both the peripheral blood and bronchoalveolar niche of pediatric patients with RMPP, thereby offering valuable mechanistic insights into the host response to M. pneumoniae infection and factors that contribute to refractory disease.