Functional genomic characterization of anti-phage defense systems in vancomycin-resistant Enterococcus faecium

Expression of AbiE in vancomycin-resistant Enterococcus faecium decreased susceptibility to two Enterococcus-targeting phages, linking one candidate defense gene to reduced phage killing.

• Why it matters: VREfm infections are difficult to treat and phage therapy is emerging, but the anti-phage defense genes in clinical VREfm isolates are poorly mapped to functional resistance.
• What they did: The study screened 21 hybrid-assembled VREfm clinical isolate genomes using DefenseFinder and PADLOC, then performed phage susceptibility testing with four lytic phages and developed a co-incubation assay to measure phage survival.
• The result: Genome-based predictions and lytic susceptibility tests showed no robust associations, while the co-incubation assay identified over two dozen phage-killing–associated genes and functional validation narrowed candidates to four tested in enterococci, including AbiE.

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