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

Reviewer #1 (Public Review):

Summary:

This is an interesting study that performs scRNA-Seq on infected and uninfected wounds. The authors sought to understand how infection with E. faecalis influences the transcriptional profile of healing wounds. The analysis demonstrated that there is a unique transcriptional profile in infected wounds with specific changes in macrophages, keratinocytes, and fibroblasts. They also speculated on potential crosstalk between macrophages and neutrophils and macrophages and endothelial cells using NicheNet analysis and CellChat. Overall the data suggest that infection causes keratinocytes to not fully transition which may impede their function in wound healing and that the infection greatly influenced the transcriptional profile of macrophages and how they interact with other cells.

Strengths:

It is a useful dataset to help understand the impact of wound infection on the transcription of specific cell types. The analysis is very thorough in terms of transcriptional analysis and uses a variety of techniques and metrics.

Weaknesses:

Some drawbacks of the study are the following. First, the fact that it only has two mice per group, and only looks at one time point after wounding decreases the impact of the study. Wound healing is a dynamic and variable process so understanding the full course of the wound healing response would be very important to understand the impact of infection on the healing wound. Including unwounded skin in the scRNA-Seq would also lend a lot more significance to this study. Another drawback of the study is that mouse punch biopsies are very different than human wounds as they heal primarily by contraction instead of re-epithelialization like human wounds. So while the conclusions are generally supported the scope of the work is limited.

Reviewer #2 (Public Review):

Summary:

The authors have performed a detailed analysis of the complex transcriptional status of numerous cell types present in wounded tissue, including keratinocytes, fibroblasts, macrophages, neutrophils, and endothelial cells. The comparison between infected and uninfected wounds is interesting and the analysis suggests possible explanations for why infected wounds are delayed in their healing response.

Strengths:

The paper presents a thorough and detailed analysis of the scRNAseq data. The paper is clearly written and the conclusions drawn from the analysis are appropriately cautious. The results provide an important foundation for future work on the healing of infected and uninfected wounds.

Weaknesses:

The analysis is purely descriptive and no attempt is made to validate whether any of the factors identified are playing functional roles in wound healing. The experimental setup is analyzing a single time point and does not include a comparison to unwounded skin.