A single-cell atlas of E. faecalis wound infection reveals novel bacterial-host immunomodulatory mechanisms

Wound infections are highly prevalent, and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites. Enterococcus faecalis is often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed single-cell RNA sequencing (scRNA-seq) on infected wounds in comparison to uninfected wounds in a mouse model. Examining over 23,000 cells, we created a comprehensive single-cell atlas that captures the cellular and transcriptomic landscape of these wounds. Our analysis revealed unique transcriptional and metabolic alterations in infected wounds, elucidating the distinct molecular changes associated with bacterial infection compared to the normal wound healing process. We identified dysregulated keratinocyte and fibroblast transcriptomes in response to infection, jointly contributing to an anti-inflammatory environment. Notably, E. faecalis infection prompted a premature, incomplete epithelial-to-mesenchymal transition in keratinocytes. Additionally, E. faecalis infection modulated M2-like macrophage polarization by inhibiting pro-inflammatory resolution in vitro , in vivo, and in our scRNA-seq atlas. Furthermore, we discovered macrophage crosstalk with neutrophils, which regulates chemokine signaling pathways, while promoting anti-inflammatory interactions with endothelial cells. Overall, our findings offer new insights into the immunosuppressive role of E. faecalis in wound infections. Wound infections, including diabetic foot ulcers, burns, or surgical sites, often lead to prolonged healing and significant health and economic burdens. Among the bacteria implicated in these persistent wounds, Enterococcus faecalis remains a relatively enigmatic player. To unravel its role in non-healing wounds, we used single-cell RNA sequencing in a mouse model, scrutinizing over 23,000 cells to construct a comprehensive single-cell map of infected wounds compared to uninfected wounds. Our investigation revealed distinct genetic and metabolic alterations in infected wounds, in which infection resulted in a perturbed inflammatory environment delayed wound healing signatures. Specifically, E. faecalis infection induces a premature and incomplete transition in keratinocytes, impeding their healing function. Furthermore, infection influences the behavior of immune cells like macrophages, affecting the body’s response to the infection. These findings not only shed light on E. faecalis ’s role in delayed wound healing but also offer potential avenues for future treatments, providing valuable insights into the challenging realm of wound infections.