Characterization of Staphylococcus epidermidis clinical and commensal isolates transcriptome upon interaction with human blood. Characterization of Staphylococcus epidermidis clinical and commensal isolates transcriptome upon interaction with human blood

The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections, resulting in increased morbidity and mortality rates. This has to do, in part, with the difficulty to accurately diagnose S. epidermidis bloodstream infections. S. epidermidis is a ubiquitous commensal of human skin and mucosa and, thus, a positive blood culture does not always represent an infection, possibly being the result of contamination during blood collection. As such, there is a high demand to find markers that can help clinicians to distinguish infection (clinical isolates) from contamination (commensal strains). With that in mind, several studies comparing phenotypic or genetic characteristics of clinical and commensal isolates have been performed over the years. However, because S. epidermidis virulence factors seem to be the same that confer its fitness as a commensal, we hypothesized that the ability of S. epidermidis strains to adapt to the host environment may not depend on a specific phenotypic and/or genetic makeup, but rather on the regulation of gene transcription. Thus, using RNA-Sequencing (RNA-seq), we characterized the transcriptome of commensal and clinical isolates in the context of infection to try to uncover differences and, thus, identify markers that could be used for the diagnostics. Several markers with the potential to discriminate between both groups were highlighted. Nevertheless, when the results obtained were confirmed in a wider collection of clinical and commensal isolates the discriminatory power of the genes initially identified was lost. Although we cannot rule out that the characterization of a larger collection of isolates would identify potential candidates, our transcriptomic data was not able to confirm our initial hypothesis, evidencing S. epidermidis opportunistic nature. Overall design: The transcriptome of the cells released from biofilms formed by three S. epidermidis clinical and three commensal isolates was characterized upon incubation with human blood for 2h at 37 oC and with agitation at 80 rpm. Each condition under test was analyzed once by RNA-seq, however, each sample analyzed was prepared by mixing total RNA from three independent assays.

定植于医疗器械表面的表皮葡萄球菌（Staphylococcus epidermidis, S. epidermidis）生物膜释放的菌体，与血流感染的发生密切相关，可导致患者发病率与死亡率升高。这在一定程度上源于表皮葡萄球菌血流感染的精准诊断难题：表皮葡萄球菌是人体皮肤与黏膜的普遍共生菌，因此血液培养阳性并不总能代表感染，也可能是采血过程中污染所致。因此，临床亟需可帮助医师区分感染菌株（临床分离株）与污染菌株（共生株）的生物标志物。
基于此，多年来已有多项研究针对临床分离株与共生株的表型或遗传特征展开对比分析。然而，由于表皮葡萄球菌的毒力因子似乎与其作为共生菌的定植适应性所需因子一致，我们提出假设：表皮葡萄球菌菌株适应宿主环境的能力，并非依赖特定的表型或遗传组成，而是取决于基因转录调控。为此，我们采用RNA测序（RNA-Sequencing, RNA-seq）技术，在感染情境下对共生株与临床分离株的转录组进行表征，以期挖掘二者的差异并筛选可用于临床诊断的生物标志物。研究初步筛选出若干具备区分两组菌株潜力的标志物。然而，当在更大规模的临床分离株与共生株集合中验证所得结果时，最初鉴定的基因的区分能力不复存在。尽管我们无法排除扩大菌株集合的表征工作可筛选出潜在候选标志物的可能性，但本研究的转录组数据未能验证最初的假设，这也印证了表皮葡萄球菌的机会致病菌特性。
实验整体设计：将3株表皮葡萄球菌临床分离株与3株共生株形成的生物膜释放的菌体，置于37℃、80 rpm振荡条件下与人体血液共孵育2小时后，对其转录组进行表征。所有待测条件均通过RNA-seq完成单次分析，且每份待测样本均由3次独立实验提取的总RNA混合制备而成。