Subinhibitory Concentrations of Ciprofloxacin Enhance Antimicrobial Resistance and Pathogenicity of Enterococcus faecium

Abstract

Enterococcus faecium has emerged as a major opportunistic pathogen for 2 decades with the spread of hospital-adapted multidrug-resistant clones. As members of the intestinal microbiota, they are subjected to numerous bacterial stresses, including antibiotics at subinhibitory concentrations (SICs). Since fluoroquinolones are extensively prescribed, SICs are very likely to occur in vivo, with potential effects on bacterial metabolism with subsequent modulation of opportunistic traits. The aim of this study was to evaluate globally the impact of SICs of ciprofloxacin on antimicrobial resistance and pathogenicity of E. faecium. Transcriptomic analysis was performed by RNA sequencing (RNA-seq) (HiSeq 2500; Illumina) using the vanB-positive reference strain E. faecium Aus0004 in the absence or presence of ciprofloxacin SIC (0.38 mg/liter, i.e., 1/8 of the MIC). Several genetic and phenotypic tests were used for validation. In the presence of ciprofloxacin SIC, 196 genes were significantly induced, whereas 286 genes were significantly repressed, meaning that 16.8% of the E. faecium genome was altered. Among upregulated genes, EFAU004_02294 (fold change, 14.3) encoded a protein (Qnr of E. faecium [EfmQnr]) homologue of Qnr proteins involved in quinolone resistance in Gram-negative bacilli. Its implication in intrinsic and adaptive fluoroquinolone (FQ) resistance in E. faecium was experimentally ascertained. Moreover, EFAU004_02292, coding for the collagen adhesin Acm, was also induced by the SIC of ciprofloxacin (fold change, 8.2), and higher adhesion capabilities were demonstrated phenotypically. Both EfmQnr and Acm determinants may play an important role in the transition from a commensal to a pathogenic state of E. faecium that resides in the gut of patients receiving fluoroquinolone therapy.KEYWORDS transcriptome, RNA-seq, fluoroquinolones, E. faecium, VRE, Qnr, Acm A lthough considered to be slightly virulent since they are natural inhabitants of the gastrointestinal tract of humans, enterococci have emerged as major opportunistic pathogens, now being responsible for 5 to 10% of hospital-acquired infections and numerous outbreaks (1). In addition, there is a spread of vancomycin-resistant enterococcus (VRE) clinical isolates, especially within the species Enterococcus faecium, which is increasingly reported (2). Notably, E. faecium is part of the ESKAPE (E. faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) multidrug-resistant (MDR) opportunistic pathogens (3). The epidemiological success of E. faecium mainly results from the

Dwarfs in disguise: multiple spinal abscesses and spondylodiscitis caused by an Enterococcus faecium small-colony variant

“…Ciprofloxacin resistance as in our case is a common trait in E. faecium and is found in the majority of strains isolated in Germany [12]. Subinhibitory dosing of ciprofloxacin has previously been described to induce SCV formation and the expression of adhesion factors facilitating pathogen persistence [13,14]. Thus, the high ciprofloxacin MIC of the BK001612 E. faecium strain might have contributed to expression of the SCV phenotype.…”

Chlortetracycline and florfenicol induce expression of genes associated with pathogenicity in multidrug-resistant Salmonella enterica serovar Typhimurium

“…Survival and persistence of bacteria following exposure to subinhibitory antibiotic concentrations is often attributed to the SOS response [ 35 – 38 ]. However, differential gene expression for genes associated with the SOS response did not indicate a coordinated response following exposure to CTC or florfenicol (Additional file 4 : Figure S3).…”

Production of Membrane Vesicles by Enterococcus faecium Cultured With or Without Subinhibitory Concentrations of Antibiotics and Their Pathological Effects on Epithelial Cells

“…Antibiotics modulate bacterial physiology regarding bacterial growth, gene transcription, and toxin production at subinhibitory concentrations (Goh et al, 2002; Yim et al, 2011; Moura et al, 2015; Ramos et al, 2015; Sinel et al, 2017). This study demonstrates that antibiotics at subinhibitory concentrations can modulate the biogenesis and proteomes of MVs in E. faecium .…”