The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection.
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection.
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DOI：
10.1186/s12866-020-02041-w
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发表时间：
2020-11-26
期刊：
影响因子：
4.2
通讯作者：
Stegger M
中科院分区：
文献类型：
--
作者：
Rendboe AK;Johannesen TB;Ingham AC;Månsson E;Iversen S;Baig S;Edslev S;Jensen JS;Söderquist B;Andersen PS;Stegger M
虽然通常被认为是人类共生菌，但表皮葡萄球菌也是一种机会性病原体，可导致与异物材料和免疫低下患者相关的医院感染。感染通常是由多药耐药(MDR)谱系引起的，这些谱系难以治疗且费用高昂，可能对患者的生活质量产生重大不利影响。异质性在携带者和感染中都是一种常见的现象，但目前检测这一现象的方法费力或昂贵。在这项研究中，我们提出了一种不依赖于培养的方法，标记为Epidome，基于扩增子测序方法，以传递初级样本物种水平之外的信息，并阐明表皮链霉菌群落的克隆、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的>； 800基因的评估，我们确定了具有可变区的基因，这些基因结合起来有助于在计算机中观察到的系统发育簇的分化，并使分类能够向下延伸到谱系水平。设计了一种结合扩增子测序的双重PCR和一条下游分析管道，以提供原始样本的亚种信息。此外，还设计了一种基于探针的定量聚合酶链式反应，以提供有价值的表皮葡萄球菌绝对丰度的定量。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，灵敏度为<； 10Copes/μL。该方法进一步应用于一组原始皮肤和鼻部样本，揭示了表皮葡萄球菌种群的高度异质性。此外，定量聚合酶链式反应显示表皮葡萄球菌的绝对丰度有很高的变异。Epidome方法用于初级样本，以获得有关表皮葡萄球菌丰度和物种水平以外的多样性的重要信息，以回答有关院内谱系的出现和传播、调查表皮葡萄球菌群落的克隆、种群动态和生态位选择等问题。我们的靶向测序方法可以在低生物量样本(如皮肤样本)中快速区分和识别临床上重要的医院谱系。网上版载有补充材料，可在10.1186/s12866-020-02041-w查阅。
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. The online version contains supplementary material available at 10.1186/s12866-020-02041-w.
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影响因子：
3
作者：
Iwase, Tadayuki;Seki, Keiko;Masuda, Shogo
通讯作者：
Masuda, Shogo
影响因子：
3.3
作者：
Méric G;Miragaia M;de Been M;Yahara K;Pascoe B;Mageiros L;Mikhail J;Harris LG;Wilkinson TS;Rolo J;Lamble S;Bray JE;Jolley KA;Hanage WP;Bowden R;Maiden MC;Mack D;de Lencastre H;Feil EJ;Corander J;Sheppard SK
通讯作者：
Sheppard SK
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
影响因子：
11.8
作者：
Li, Xiqi;Arias, Cesar A.;Shelburne, Samuel A.
通讯作者：
Shelburne, Samuel A.
影响因子：
4.1
作者：
Hellmark, Bengt;Soderquist, Bo;Nilsdotter-Augustinsson, Asa
通讯作者：
Nilsdotter-Augustinsson, Asa