Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance

Clara Sinel (1) , Yoann Augagneur (2) , Mohamed Sassi (2) , Julie Bronsard (2) , Margherita Cacaci (3) , Francois Guerin (4, 1) , Maurizio Sanguinetti (3) , Pierrick Meignen (5) , Vincent Cattoir (4, 1) , Brice Felden (2)

1 U2RM - Unité de Recherche Risques Microbiens
2 BRM - ARN régulateurs bactériens et médecine
3 Unicatt - Università cattolica del Sacro Cuore [Milano]
4 CHU Caen
5 UNICAEN - Université de Caen Normandie

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.

Domains: Life Sciences [q-bio]; Microbiology and Parasitology

Clara Sinel, Yoann Augagneur, Mohamed Sassi, Julie Bronsard, Margherita Cacaci, et al.. Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance. Scientific Reports, 2017, 7 (1), pp.11067. ⟨10.1038/s41598-017-11265-2⟩. ⟨hal-01619295⟩