Austin Centre for Infection Research, Infectious Diseases Department, Austin Health, Heidelberg, Victoria, Australia.
Antimicrob Agents Chemother. 2013 Aug;57(8):3864-74. doi: 10.1128/AAC.00263-13. Epub 2013 Jun 3.
The critical role of noncoding small RNAs (sRNAs) in the bacterial response to changing conditions is increasingly recognized. However, a specific role for sRNAs during antibiotic exposure has not been investigated in Staphylococcus aureus. Here, we used Illumina RNA-Seq to examine the sRNA response of multiresistant sequence type 239 (ST239) S. aureus after exposure to four antibiotics (vancomycin, linezolid, ceftobiprole, and tigecycline) representing the major classes of antimicrobials used to treat methicillin-resistant S. aureus (MRSA) infections. We identified 409 potential sRNAs and then compared global sRNA and mRNA expression profiles at 2 and 6 h, without antibiotic exposure and after exposure to each antibiotic, for a vancomycin-susceptible strain (JKD6009) and a vancomycin-intermediate strain (JKD6008). Exploration of this data set by multivariate analysis using a novel implementation of nonnegative matrix factorization (NMF) revealed very different responses for mRNA and sRNA. Where mRNA responses clustered with strain or growth phase conditions, the sRNA responses were predominantly linked to antibiotic exposure, including sRNA responses that were specific for particular antibiotics. A remarkable feature of the antimicrobial response was the prominence of antisense sRNAs to genes encoding proteins involved in protein synthesis and ribosomal function. This study has defined a large sRNA repertoire in epidemic ST239 MRSA and shown for the first time that a subset of sRNAs are part of a coordinated transcriptional response to specific antimicrobial exposures in S. aureus. These data provide a framework for interrogating the role of staphylococcal sRNAs in antimicrobial resistance and exploring new avenues for sRNA-based antimicrobial therapies.
非编码小 RNA（sRNAs）在细菌对环境变化的反应中起着关键作用，这一点正日益得到人们的认可。然而，在金黄色葡萄球菌中，sRNA 在抗生素暴露过程中所起的特定作用尚未得到研究。在这里，我们使用 Illumina RNA-Seq 技术，研究了多药耐药性 239 型（ST239）金黄色葡萄球菌在暴露于万古霉素、利奈唑胺、头孢洛林和替加环素四种抗生素后，sRNA 的反应情况，这四种抗生素代表了用于治疗耐甲氧西林金黄色葡萄球菌（MRSA）感染的主要抗菌药物类别。我们鉴定了 409 个潜在的 sRNA，然后在没有抗生素暴露的情况下以及在暴露于每种抗生素 2 小时和 6 小时后，比较了敏感株（JKD6009）和中介株（JKD6008）的全局 sRNA 和 mRNA 表达谱。使用非负矩阵分解（NMF）的一种新实现方法对这个数据集进行多元分析的探索，揭示了 mRNA 和 sRNA 的反应非常不同。其中，mRNA 的反应与菌株或生长阶段条件聚类，而 sRNA 的反应则主要与抗生素暴露有关，包括对特定抗生素具有特异性的 sRNA 反应。抗菌反应的一个显著特点是，编码参与蛋白质合成和核糖体功能的蛋白质的基因的反义 sRNA 非常突出。本研究在流行的 ST239 型 MRSA 中定义了一个庞大的 sRNA 库，并首次表明，sRNA 是金黄色葡萄球菌对特定抗菌药物暴露的协调转录反应的一部分。这些数据为研究金黄色葡萄球菌 sRNA 在抗菌耐药性中的作用提供了一个框架，并为基于 sRNA 的抗菌治疗探索新途径。
