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

Abstract

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 with wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.

Methods: A bioinformatics pipeline was developed to compare the sequences of transposons containing vanB resistance genes. This pipeline was used in addition to wgMLST to investigate two separate ongoing VRE outbreaks. Five separate colonies from 15 different samples and 10 vancomycin-susceptible isolates were also sequenced.

Findings: Of 46 strains collected during two outbreaks, 26 and nine strains were identified as being part of the two outbreaks based on wgMLST clustering. In six strains an identical vanB transposon but a different wgMLST cluster were identified, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. There was no evidence of variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. One vancomycin-susceptible E. faecium in blood culture was identified, with a wgST similar to one of the outbreak strains.

Conclusion: 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.

Keywords: Enterococcus faecium; Hospital outbreak; Mobile genetic elements; Transposon; Vancomycin resistance; Whole-genome sequencing.