Pangenomics insights of enterococcus faecium human isolates and identification of novel therapeutic targets by in silico subtractive genomics.

Enterococcus faecium is a Gram-positive bacteria that infects the human gastrointestinal tract and it is a leading cause of hospital-acquired infections, due to its ability to cause various types of infections, such as endocarditis, bacteremia, urinary tract infections, and others, exacerbated by its multidrug resistance, notably to vancomycin. Because they are linked to major infections that are difficult to manage, and also due to the widespread acquisition of resistance genes, management remains difficult. This study employs pangenomic analyses and subtractive genomics to explore genetic diversity and identify novel therapeutic targets across 20 human-derived E. faecium genomes. Phylogenomic analyses revealed four distinct clades, with genomic rearrangements and horizontal gene transfer events underscoring adaptive evolution. Comparative genomics identified 20 pathogenicity islands and 12 resistance islands, alongside pan-resistome profiling highlighting prevalent resistance to aminoglycosides, elfamycins, and glycopeptides (e.g., vancomycin in 14/20 strains). Core genome analyses, filtered for non-human homologs, prioritized cytoplasmic proteins critical for survival. Subtractive genomics predicted five high-confidence drug targets: phosphocarrier protein HPr (metabolic regulation), GNAT family N-acetyltransferase (antibiotic resistance), translation initiation factor IF-1 (protein synthesis), HU family DNA-binding protein (genome stability), and a sugar-binding domain protein (nutrient uptake). Structural modeling identified these targets as druggable with conserved roles in bacterial viability. This integrative approach elucidates E. faecium's genomic plasticity and resistance mechanisms while proposing candidates for targeted therapies, addressing the urgent need for novel interventions against this resilient pathogen.