Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients’ quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis. The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.

中文翻译：

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Epidome - 评估表皮葡萄球菌定植和感染的种群结构和异质性的物种特异性方法


虽然表皮葡萄球菌通常被称为人类共生菌，但它也是一种机会性病原体，可引起与异物和免疫功能低下患者相关的医院感染。感染通常由多重耐药 (MDR) 谱系引起，治疗起来困难且成本高昂，并且可能对患者的生活质量产生重大不利影响。异质性是携带和感染中的常见现象，但目前检测这种现象的方法既费力又昂贵。在这项研究中，我们提出了一种独立于培养的方法，标记为 Epidome，基于扩增子测序方法，可在原始样本上提供超出物种水平的信息，并阐明表皮葡萄球菌群落的克隆性、种群结构和时间稳定性或生态位选择。基于对表皮葡萄球菌核心基因组中超过 800 个基因的评估，我们鉴定了具有可变区的基因，这些基因的组合促进了在计算机中观察到的系统发育簇的分化，并允许分类到谱系水平。双重 PCR 与扩增子测序方案相结合，以及下游分析流程旨在提供来自原始样本的亚种信息。此外，基于探针的 qPCR 旨在提供有价值的表皮葡萄球菌绝对丰度定量。该方法在代表皮肤共生体的分离株和基因组模拟群落上进行了验证，灵敏度 < 10 拷贝/μL。该方法还应用于原始皮肤和鼻腔样本的样本集，揭示了表皮葡萄球菌种群的高度异质性。此外，qPCR 显示表皮葡萄球菌的绝对丰度存在高度变化。 Epidome 方法设计用于初级样本，以获得超越物种水平的表皮葡萄球菌丰度和多样性的重要信息，以回答有关院内谱系的出现和传播的问题，调查表皮葡萄球菌群落的克隆性、种群动态和生态位选择。我们的靶向测序方法可以快速区分和鉴定低生物量样品（例如皮肤样品）中临床重要的院内谱系。