Elucidating vancomycin-resistant E. faecium outbreaks: the role of clonal spread and movement of mobile genetic elements.

Introduction: Vancomycin resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. Outbreaks are mainly caused by vanA or vanB VREfm. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons. We aimed to combine vanB-carrying transposons characteristics with core-genome multi-locus sequence typing (cgMLST) typing and epidemiological data to understand the pathways of transmission in in nosocomial outbreak clusters. Methods: Retrospectively, 36 VREfm isolates obtained from 34 patients during VREfm outbreaks in 2014 were analysed. Isolates were sequenced on a MiSeq instrument and de novo assembled by CLC Genomics Workbench. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points were performed using ACT and multiple blast analyses.Results Four different vanB transposons were found among the isolates. CgMLST divided sequence type (ST) 80 isolates into three cluster types (CT); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging CT103 two different vanB transposons were found. On the contrary, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon. Combining cgMLST and transposon analysis results led to new insights how to look at VREfm outbreaks. Conclusion: CgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows to investigate both clonal spread as well as the spread of MGEs which will lead to a better insight and understanding of the complex transmission routes in VREfm outbreaks.