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

The aim of the study was to develop and validate a real-time PCR-assay detecting the sequence bridging Tn1549 and the E. faecium chromosome in the emerging vanB Vancomycin-resistant Enterococcus faecium (VREfm) clone (ST80/CT2406). The Transposon 1549 (Tn1549) insertion site was determined on routinely sequenced VREfm isolates. The outer boundaries of Tn1549 and adjoining host bacterial sequences were determined using BLAST search. A silent information regulator (sir2) gene was discovered. Next, the primers and probes 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 in rectal screening samples submitted to our laboratory. The PCR-assay proved to be accurate and provide rapid diagnostic of the emerging vanB VREfm in rectal screening samples.