Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium

Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is recommended for molecular typing. Long-read sequence is more rapid and provides useful information about the structural composition of the genome, but lacks the precision required for SNP-based typing methods. Here we compared prophages among 50 complete genome sequences of E. faecium belonging to different lineages to explore whether a signature of phage content would be usable for typing and identifying an outbreak caused by this pathogen. As a proof of principle, we investigated if long-read sequencing data of 12 isolates allows for the identification of phage signatures.