Enterococcus faecium has become a major opportunistic pathogen with the emergence of vancomycin-resistant enterococci (VRE). As part of the gut microbiota, they have to cope with numerous stresses, including effects of antibiotics and other xenobiotics, especially in patients hospitalized in intensive care units (ICUs) who receive many medications. The aim of this study was to investigate the impact of the most frequently prescribed xenobiotics for ICU patients on fitness, pathogenicity, and antimicrobial resistance of the vanB-positive E. faecium Aus0004 reference strain. Several phenotypic analyses were carried out, and we observed that caspofungin, an antifungal agent belonging to the family of echinocandins, had an important effect on E. faecium growth in vitro. We confirmed this effect by electron microscopy and peptidoglycan analysis and showed that, even at a subinhibitory concentration (1/4× MIC, 8 mg/liter), caspofungin had an impact on cell wall organization, especially with respect to the abundance of some muropeptide precursors. By transcriptome sequencing (RNA-seq), it was also shown that around 20% of the transcriptome was altered in the presence of caspofungin, with 321 and 259 significantly upregulated and downregulated genes, respectively. Since the fungal target of caspofungin (i.e., β-1,3-glucan synthase) was absent in bacteria, the mechanistic pathway of caspofungin activity was investigated. The repression of genes involved in the metabolism of pyruvate seemed to have a drastic impact on bacterial cell viability, while a decrease of glycerol metabolism could explain the conformational modifications of peptidoglycan. This is the first report of caspofungin antibacterial activity against E. faecium, highlighting the potential impact of nonantibiotic xenobiotics against bacterial pathogens.

中文翻译：

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意外的细胞壁改变介导的抗真菌药卡泊芬净对耐万古霉素的粪肠球菌的杀菌活性。

随着耐万古霉素肠球菌（VRE）的出现，粪便肠球菌已成为主要的机会病原体。作为肠道菌群的一部分，它们必须应对众多压力，包括抗生素和其他异源生物的影响，尤其是在重症监护病房（ICU）住院并接受许多药物治疗的患者中。这项研究的目的是调查对ICU患者最常用的异生素对vanB阳性粪肠球菌Aus0004参考菌株的适应性，致病性和抗菌素耐药性的影响。进行了数种表型分析，我们观察到卡泊芬净是一种棘手的粪便，对大肠杆菌具有重要影响生长在体外。我们通过电子显微镜和肽聚糖分析证实了这种作用，并表明，即使在亚抑制浓度（1/4×MIC，8 mg / L）下，卡泊芬净也对细胞壁组织有影响，特别是在某些多聚肽方面前体。通过转录组测序（RNA-seq），还显示在卡泊芬净存在下，约有20％的转录组发生了改变，分别有321和259个基因显着上调和下调。由于细菌中不存在卡泊芬净的真菌靶标（即β-1,3-葡聚糖合酶），因此研究了卡泊芬净活性的机理。丙酮酸代谢相关基因的抑制似乎对细菌细胞的生存能力产生了巨大影响，而甘油代谢的下降可以解释肽聚糖的构象修饰。这是卡泊芬净抗细菌活性的首次报道屎肠球菌，突出了非抗生素异生素对细菌病原体的潜在影响。