Omics approach to multi-resistant clinical vanB2 Enterococcus faecalis strain. Authors: Luís Pinto, Carmen Torres, Concha Gil, Hugo Santos, Jose Capelo-Martínez, Vítor Borges, João Paulo Gomes, Catarina Silva, Luís Vieira, Patricia Poeta, Gilberto Igrejas. vanB2 Enterococcus faecalis C2620

In this study was conducted a detailed proteomic and transcriptomic research on a clinically relevant Vancomycin-resistant Enterococcus (VRE) strain isolated from a patient with urinary tract infection. Previous genotypic profile revealing the presence of resistance genes, with special relevance to the vanB cluster, led us to the development of whole genome sequencing and RNA sequencing (RNA-Seq) in order to detect and quantify the genes expressed by our pathogenic strains. Afterwards, was performed the proteomic identification and comparison methods of both membrane and cytoplasmic sub-proteomes by two-dimensional gel electrophoresis followed by matrix-assisted laser desorption/ionization – time of flight / mass spectrometry. In our work, we have obtained two sub-proteomes (membrane and cytoplasm) of a VRE faecalis strain of clinical background where 118 proteins were identified within a total of 207 spots and confronted to the results obtained by the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified as well as linked to antibiotic and drug response, which is consistent with the state of multi-resistance previously described and so highlighting the serious health problem found in hospitals worldwide. Even though the expression levels are yet not consistent between omics, the information obtained is of much value towards understanding the mechanisms behind antibiotic resistance and virulent bacteria survival capacities.

本研究针对一例从尿路感染患者体内分离得到的临床相关耐万古霉素肠球菌（Vancomycin-resistant Enterococcus, VRE）菌株，开展了系统性蛋白质组学与转录组学研究。此前的基因型分析显示该菌株携带耐药基因，其中vanB基因簇具有关键临床意义，为此我们开展了全基因组测序与RNA测序（RNA-Seq），以检测并定量该致病菌株的表达基因。随后，我们通过二维凝胶电泳结合基质辅助激光解吸电离-飞行时间质谱（matrix-assisted laser desorption/ionization – time of flight / mass spectrometry），完成了膜蛋白亚组与胞质蛋白亚组的蛋白质组学鉴定与比较分析。本研究获得了一株临床来源的粪肠球菌VRE菌株的两类蛋白亚组（膜蛋白组与胞质蛋白组），在总计207个蛋白斑点中鉴定出118种蛋白质，并将该结果与全转录组测序分析所得结果进行了比对。研究鉴定出多个与应激及细胞应答相关的基因与蛋白质，同时这些分子也与抗生素及药物应答密切相关，这与此前报道的多重耐药表型一致，进而凸显了全球医疗机构中普遍存在的严重公共卫生问题。尽管两组组学数据的表达水平尚未完全一致，但本研究所得信息对于解析抗生素耐药机制与致病菌存活能力的内在机理具有重要学术价值。