Development of a PCR assay for rapid and accurate detection of an emerging vanB Enterococcus faecium clone in the Capital Region of Denmark

Objectives: To develop and validate a real-time PCR assay detecting the sequence bridging Tn1549 and the Enterococcus faecium chromosome in the emerging vanB vancomycin-resistant E. faecium (VREfm) clone (ST80/CT2406). Methods: The Tn1549 insertion site was determined on routinely sequenced VREfm isolates. The outer boundaries of Tn1549 and adjoining host bacterial sequences were determined using a BLAST search in the silent information regulator gene sir2. Next, the primers and probe were developed, targeting the sequence bridging Tn1549 and the E. faecium chromosome. Finally, the PCR assay was validated on well-characterized strains and prospectively performed on rectal screening samples submitted to our laboratory. Results and conclusions: The PCR assay proved to be accurate and provide rapid diagnosis of the emerging vanB VREfm in rectal screening samples.