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

ABSTRACT:

Background

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 often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates.

Results

Analysis of

SUBMITTER: Lisotto P 

PROVIDER: S-EPMC8542323 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature