Expansion of Vancomycin-resistant Enterococcus faecium in an academic tertiary hospital in Southwest Germany: a large-scale whole genome-based outbreak investigation

Abstract

Background: Vancomycin-resistant Enterococcus faecium (VRE fm) is a frequent cause of nosocomial outbreaks. In the second half of 2015 a sharp increase in the incidence of VRE fm was observed at our university medical center. Next-generation sequencing (NGS) was used to analyze the first isolates of VRE fm recovered from patients between 2010 and 2016 (n=773) in order to decipher epidemiological change, outbreak dynamics, and possible transmission routes.

Materials and methods: VRE fm isolates were analyzed using whole genome sequencing followed by sequence type extraction, and phylogenetic analysis. We examined epidemiological data, room occupancy data, and patient transferals and calculated an intensity score for patient-to-patient contact.

Results: Phylogenetic analysis revealed the presence of 38 NGS clusters and 110 single clones. The increase of VRE fm was mainly caused by the expansion of two newly introduced NGS clusters, comprising VanB-type strains of the MLST sequence type (ST)80 and ST117. Combining phylogenetic information with epidemiological data, intra-hospital transmission could be demonstrated, however to a lesser extent than initially expected based solely on epidemiological data. The outbreak clones were continuously imported from other hospitals, suggesting a change of the epidemiological situation at a regional scale. Tracking intra-hospital patient transferals, two major axes could be identified that contributed to the spread of VRE fm within the hospital.

Conclusions: NGS-based outbreak analysis revealed a dramatic change in the local and regional epidemiology of VRE fm, emphasizing the role of healthcare networks in the spread of VRE fm.