VanB transposon analysis detects horizontal gene transfer in vancomycin resistant Enterococcus faecium: description of two outbreaks.

Background: Outbreaks with vancomycin resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation.

Aim: Developing a method for sequence analysis of vancomycin resistance genes in parallel to wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.

Methods: We developed a bioinformatics pipeline to compare the sequences of transposons containing vanB resistance genes. We used this pipeline in addition to wgMLST to investigate two separate ongoing VRE outbreaks. We also sequenced five separate colonies from 15 different samples and 10 vancomycin sensitive isolates.

Findings: Of 46 strains collected during two outbreaks, we identified 26 and 9 strains to be part of the two outbreaks based on wgMLST clustering. In 6 strains we identified an identical vanB transposon but a different wgMLST cluster, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. We found no variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. We identified 1 vancomycin sensitive E. faecium in blood culture with a similar wgST as one of the outbreak strains.

Conclusions: Real-time analysis of transposons containing vancomycin resistance genes provides additional information for analysis of vanB-VRE outbreaks. It detects possible horizontal gene transfer which would not be detected using conventional methods. Transposon analysis is a valuable addition to whole genome sequence analysis during vanB-VRE outbreaks.