Abstract
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.
Highlights
Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks
Using the DETR’PROK workflow, a pipeline devoted to sRNA identification in prokaryotes, combined with an in silico search for the conserved sRNAs in bacteria and RNA-seq depth testing within the intergenic regions (IGRs), we identified 61 sRNA candidates
To investigate the presence of these molecules in this species, we studied the E. faecium Aus0004 reference strain, a vanB-positive clonal complex 17 (CC17) clinical isolate recovered from a bloodstream infection in Australia[27]
Summary
Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. 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. Enterococcus faecalis and Enterococcus faecium have emerged as major opportunistic pathogens[2] They have become resistant to numerous antibiotics[3], with the spread of vancomycin-resistant enterococci (VRE), especially in E. faecium[4]. Thanks to its huge genomic plasticity and metabolic versatility, E. faecium is a highly adapted commensal bacterial species that can turn into an opportunistic pathogen[8] Despite their paramount importance, the mechanisms involved in this physiological transition have not been adequately investigated[9]. A recent study has demonstrated that exposure to ciprofloxacin SICs enhance antimicrobial resistance and pathogenicity in E
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