Methicillin-resistant Staphylococcus aureus strain ST398 shows abundant cis-regulatory transcription with limited antisense and intergenic expression upon linezolid stress
Background: Bacterial small regulatory RNAs (sRNAs) have been implicated in important processes including antimicrobial stress response. However, the full extent of sRNA involvement in antimicrobial response in Staphylococcus aureus, an important pathogen, is incompletely understood. We investigated the transcriptional profiles of a linezolid-resistant, livestock-associated methicillin-resistant S. aureus (LA-MRSA) strain ST398 under conditions of linezolid stress.  Methods: Cells in mid-exponential growth were subjected to low (8 µg/ml) and high (16 µg/ml) dose linezolid treatments followed by high throughput RNA sequencing. Read mapping and differential expression analysis were performed followed by detection and interrogation of various sRNA and mRNA transcripts.  Results: Twenty-three putative regulatory RNA transcripts were expressed under low- and high-dose exposure conditions. Cis-acting regulatory elements, mainly targeting ribosomal biogenesis constituted the majority of transcriptional response with limited antisense and small RNA expression.  Conclusions: This is the first study to investigate linezolid-responsive small RNA transcription in LA-MRSA strain ST398 and the first to query regulatory RNAs on  a background of linezolid resistance. It provides preliminary insights and a basis for interrogating small RNAs in other strains in the quest to understand drug-responsive regulatory RNAs and identify potential anti-staphylococcal therapeutic candidates. Overall design: Multidrug-resistant strain of S. aureus was subjected to 2 different doses of Linezolid (0, 8 and 16ug/mL) and RNA was sequenced after 10 minutes of exposure. MHB was used as media.