A novel resistance reversion mechanism in a vancomycin-variableEnterococcus faeciumstrain

Abstract

AbstractObjectivesTo investigate an outbreak ofEnterococcus faeciumin a hospital haematology ward and uncover the mechanism of a vancomycin resistance phenotype-genotype disparity in an isolate from this outbreak.MethodsWhole genome shotgun sequencing was used for the phylogenetic analysis ofE. faeciumisolates (n = 39) and to identify the carriage of antibiotic resistance genes. A long-read sequencing approach was adopted to identify structural variations in the vancomycin resistance region of a vancomycin-variableE. faecium(VVE) and to uncover the resistance reversion mechanism in this isolate. RT-qPCR and RT-PCR were used to determine differences in the expression ofvanRSandvanHAXamong strains.ResultsTheE. faeciumstrains isolated in the hospital haematology ward were extensively drug resistant and highly diverse. The notable expansion of ST262 among patients was the likely driver of a VRE outbreak. A VVE isolate was identified that could rapidly revert to a vancomycin-resistant state in the presence of vancomycin. Disruption of thevanRgene in this isolate by an IS6-family element impaired its response to vancomycin. However, when the isolate was evolved to vancomycin resistance, it could constitutively express thevanHAXgenes at levels up to 36,000-fold greater than the parent isolate via co-transcription with a ribosomal RNA operon.ConclusionIn this study, we report a VVE isolate that was isolated during a VRE outbreak. This strain was capable of rapidly reverting to a resistant phenotype through a novel mechanism involving integration ofvanHAXdownstream of a ribosomal RNA operon. During VRE outbreaks, attention should be paid to contemporaneous vancomycin-susceptible strains as these may carry silent vancomycin resistance genes that can be activated through genomic rearrangements upon exposure to vancomycin.