Successful containment of two vancomycin-resistant Enterococcus faecium (VRE) outbreaks in a Dutch teaching hospital using environmental sampling and whole genome sequencing.

Abstract Background Vancomycin-resistant enterococci (VRE) may cause nosocomial outbreaks. We describe all VRE carriers that were identified in 2018. Aim To investigate the genetic relatedness of the VRE isolates and the possibility of a common environmental reservoir using environmental sampling and whole genome sequencing (WGS). Methods Infection control measures consisted of contact isolation, contact surveys, point prevalence screening, environmental sampling, cleaning and disinfection. VRE isolates were sequenced on a MiSeq sequencer (Illumina, San Diego, CA, USA), and assembled using SPAdes v.3.10.1. A minimal spanning tree and a neighbour joining tree based on allele diversity of cgMLST and accessory genes using Ridom SeqSphere+ software (Ridom GmbH, Munster, Germany) was created. Findings During a one year period, 19 VRE carriers were identified of whom 17 were part of two outbreaks. Before environmental cleaning and disinfection, 55 (14%) environmental samples were VRE positive. Fifty-one isolates (23 patient and 28 environmental samples) were available for WGS analysis. Forty-four isolates could be assigned to ST117-vanB, five to ST17-vanB, and two to ST80-vanB. Isolates from outbreak 1 (n=22) and outbreak 2 (n=22) both belonged to ST117-vanB, WGS, however, showed a different cluster type with 257 allelic differences. Conclusion The present study shows that WGS of two outbreak strains provided discrimination information regarding genetic relatedness and rejected the hypothesis of a common environmental reservoir. A high degree of environmental contamination was associated with more VRE transmission. Quantification of environmental contamination may reflects VRE transmission potential and could therefore support the infection control measures.