The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
The University of Connecticut Health Center, Farmington, Connecticut, USA.
mBio. 2022 Dec 20;13(6):e0263222. doi: 10.1128/mbio.02632-22. Epub 2022 Nov 21.
Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.
表皮葡萄球菌是一种广泛存在于人类共生皮肤上的细菌，也是最常见的医院获得性病原体之一。这种显著的生活方式可塑性的遗传因素尚不完全清楚，主要是由于遗传操作的困难，排除了对该物种进行高通量功能分析的可能性。为了探究表皮葡萄球菌在各种环境条件下生存的多功能性，我们开发了一种大规模的 CRISPR 干扰（CRISPRi）筛选方法，并结合了 24 种不同条件下的转录谱（RNA 测序），并试点了一种基于液滴的 CRISPRi 方法来提高通量和灵敏度。我们确定了潜在的必需基因，重要的是揭示了氨基酸代谢对在各种环境中生存的重要性，并证明了痕量金属摄取对多种胁迫条件下生存的重要性。我们鉴定了在我们的应激和营养限制条件范围内显著富集和受抑制的途径，证明了表皮葡萄球菌在应对环境胁迫方面具有相当大的可塑性。此外，我们推测了一种氮代谢与生活方式多样性之间的联系机制，以应对高渗透压挑战，例如在人类皮肤上遇到的挑战。最后，我们研究了表皮葡萄球菌在酸胁迫下的生存情况，并假设细胞壁修饰在酸性条件下的生存反应中起关键作用。总之，这项研究整合了大规模的 CRISPRi 和转录组学数据，以提供对人类皮肤微生物组关键成员的深入了解。我们的研究结果还为 CRISPRi 筛选提供了有价值的基准分析，并为其他葡萄球菌研究人员提供了丰富的资源。
表皮葡萄球菌是一种广泛存在于健康人体皮肤上的细菌，但它也是皮肤感染和与植入医疗器械相关的血流感染的常见原因。由于人体皮肤上有许多不同类型的表皮葡萄球菌，每种都含有不同的基因，我们的目标是确定这些不同的基因如何使表皮葡萄球菌从健康的皮肤生长状态转变为感染性病原体。了解这种转变对于开发预防和治疗表皮葡萄球菌感染的新策略至关重要。
