University of Caen Normandie, EA4655, Caen, France.
Inserm U1230-Biochimie pharmaceutique, Rennes University, Rennes, France.
Sci Rep. 2017 Sep 11;7(1):11067. doi: 10.1038/s41598-017-11265-2.
Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. Regulatory RNAs (sRNAs) are major players in adaptive responses, including antibiotic resistance. They were extensively studied in gram-negative bacteria, but less information is available for gram-positive pathogens. No sRNAs are described in E. faecium. We sought to identify a set of sRNAs expressed in vancomycin-resistant E. faecium Aus0004 strain to assess their roles in daptomycin response and resistance. Genomic and transcriptomic analyses revealed a set of 61 sRNA candidates, including 10 that were further tested and validated by Northern and qPCR. RNA-seq was performed with and without subinhibitory concentrations (SICs) of daptomycin, an antibiotic used to treat enterococcal infections. After daptomycin SIC exposure, the expression of 260 coding and srna genes was altered, with 80 upregulated and 180 downregulated, including 51% involved in carbohydrate and transport metabolisms. Daptomycin SIC exposure significantly affected the expression of seven sRNAs, including one experimentally confirmed, sRNA_0160. We studied sRNA expression in isogenic mutants with increasing levels of daptomycin resistance and observed that expression of several sRNAs, including sRNA_0160, was modified in the stepwise mutants. This first genome-wide sRNA identification in E. faecium suggests that some sRNAs are linked to antibiotic stress response and resistance.
屎肠球菌是医院获得性感染和暴发的主要原因。调节 RNA（sRNA）是适应性反应的主要参与者，包括抗生素耐药性。它们在革兰氏阴性菌中得到了广泛研究，但革兰氏阳性病原体的信息较少。屎肠球菌中没有描述 sRNA。我们试图鉴定一组在万古霉素耐药屎肠球菌 Aus0004 菌株中表达的 sRNAs，以评估它们在达托霉素反应和耐药性中的作用。基因组和转录组分析揭示了一组 61 个 sRNA 候选物，其中 10 个进一步通过 Northern 和 qPCR 进行了测试和验证。进行了 RNA-seq 实验，使用和不使用亚抑菌浓度（SIC）的达托霉素，达托霉素是一种用于治疗肠球菌感染的抗生素。在达托霉素 SIC 暴露后，260 个编码和 srna 基因的表达发生改变，其中 80 个上调，180 个下调，包括 51%涉及碳水化合物和运输代谢。达托霉素 SIC 暴露显著影响了 7 个 sRNA 的表达，其中包括一个经过实验证实的 sRNA_0160。我们在具有不同达托霉素耐药水平的同基因突变体中研究了 sRNA 表达，并观察到包括 sRNA_0160 在内的几个 sRNA 的表达在逐步突变体中发生了改变。这是屎肠球菌中首次进行的全基因组 sRNA 鉴定，表明一些 sRNA 与抗生素应激反应和耐药性有关。
