Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.

中文翻译：

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抗新兴病原体的多组学底物？耐万古霉素粪肠球菌临床菌株的转录组和蛋白质组概况。

抗生素耐药性和医院获得性感染在全球范围内呈上升趋势。近几十年来在临床环境中已报道了耐万古霉素的肠球菌。在这项多组学研究中，我们提供了从患有尿路感染的患者身上耐万古霉素的粪肠球菌临床分离株的蛋白质组学和转录组学分析。菌株C2620的先前基因型谱表明存在vanB簇特有的抗生素抗性基因。为了进一步研究该病原菌株的转录组，我们使用了全基因组测序和RNA测序来检测和定量表达的基因。在平行下，我们使用了二维凝胶电泳，然后使用MALDI-TOF / MS（基质辅助激光解吸/电离-飞行时间/质谱法）来鉴定蛋白质组中的蛋白质。我们分别研究了膜和细胞质子蛋白质组。从总共207个分析点中，我们鉴定出118种蛋白质。将蛋白质列表与从完整转录组分析中获得的结果进行比较。鉴定了与压力和细胞反应有关的几种基因和蛋白质，以及与抗生素和药物反应有关的一些基因和蛋白质，这与已知的多抗状态一致。即使转录组和蛋白质组数据之间的相关性尚未完全了解，