Prophage landscape in Enterococcus faecium: diversity, resistance genes, virulence factors, and endolysin profiling

Enterococcus faecium is a major opportunistic pathogen associated with healthcare-associated infections and increasing antimicrobial resistance. Prophages play critical roles in bacterial evolution by mediating horizontal gene transfer, but a comprehensive analysis of prophages in E. faecium has not been performed. A total of 495 complete E. faecium genomes were retrieved from the NCBI database. Prophages were identified and classified using PHASTEST and PhaGCN2.3 software. The interactions between prophages within host genomes were analyzed using logistic regression. Antimicrobial resistance (AMR), virulence factor (VF), and endolysin genes within intact prophages were characterized using Abricate, the VFDB, and the CARD databases. Comparative analyses were conducted between human- and animal-origin strains. A total of 2119 prophages were detected, of which 1628 were intact. Nearly all E. faecium strains (99.4%) harbored at least one prophage, with an average of 4.2 prophages per genome. Staphy_SPbeta_like (26.4%) and Lister_2389 (22.1%) were the main types of prophages. Exclusion was most prevalent pattern, and specific prophages exhibiting varying interaction profiles. Classification revealed that most prophages belonged to the Bronfenbrennervirinae subfamily and the Herelleviridae family. Among intact prophages, 20.4% carried AMR genes and 1.4% harbored VF gene, primarily the adhesin-encoding gene ecbA. Endolysin genes, detected in 59.6% of prophages, exhibited high sequence diversity. Prophage distribution and types varied significantly among different ST strains, with prophage types showing distinct patterns in carrying AMR, VF, and endolysin-encoding genes. No significant differences in AMR, VF, or endolysin genes were observed between prophages of human and animal origins. This study provides the first comprehensive genomic characterization of prophages in E. faecium, revealing their abundance, diversity, and potential roles in resistance, virulence, and evolution. These findings highlight the importance of prophages in shaping the pathogenicity and adaptability of E. faecium and underscore the need for further functional investigations.