Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012-2013 investigated by WGS, MLST and PFGE

Objectives: In Denmark, the incidence of vancomycin resistant Enterococcus faecium (VREfm) has increased since 2012. The aim of the study was to investigate epidemiology and clonal relatedness of VREfm isolates in Danish hospitals 2012 – 2013 using WGS. The second aim was to evaluate if WGS-based typing could replace PFGE for typing of VREfm. Methods: A population-based study was conducted including all VREfm isolates submitted for national surveillance from January 2012 through April 2013. All isolates were investigated by WGS, MLST and PFGE. Results: One-hundred and thirty-two isolates were included. The majority of the isolates were from clinical samples (77%). Gastroenterology/abdominal surgery (29%) and ICUs (29%) were the predominant departments with VREfm. Genomics revealed a polyclonal structure of the VREfm outbreak. Seven subgroups of 3-44 genetically closely related isolates (separated by less than 17 single nucleotide polymorphisms (SNPs)) were identified using WGS. Direct or indirect transmission of VREfm between patients and intra- and inter-regional spreading clones were observed. We identified 10 Sequence Types. PFGE identified four major clusters (13-43 isolates) and seven minor clusters (2-3 isolates). The results from the typing-methods were highly concordant. However, WGS-based typing had the highest discriminatory power. Conclusions: The study emphasizes the importance of infection control measures to limit transmission of VREfm between patients. However, the diversity of the VREfm isolates point to the fact that other important factors may also affect the VREfm increase in Denmark. Finally, WGS is suitable for typing of VREfm and has replaced PFGE for typing of VREfm in Denmark.