Multidrug-Resistant Enterococcus faecalis from Yak Feces: Isolation, Genomic Characterization and Functional Insights

<i>Enterococcus faecalis</i> (<i>E. faecalis</i>) is a significant zoonotic pathogen, primarily causing opportunistic infections in humans while often existing as a commensal in animal reservoirs, facilitating its dissemination. Current understanding of the resistance profiles, virulence mechanisms, and host-pathogen interactions of <i>E. faecalis</i> from ruminants, particularly unique species such as the plateau yak, remains limited. This knowledge gap hinders the accurate assessment of their transmission risk and the development of effective control strategies. This study presents a comprehensive analysis of a multidrug-resistant <i>E. faecalis</i> isolate from yak feces, integrating whole-genome sequencing (WGS), an animal challenge model, and transcriptomic profiling. Antimicrobial susceptibility testing revealed resistance to β-lactams, aminoglycosides, glycopeptides, tetracyclines, and fluoroquinolones. WGS identified numerous resistance genes (e.g., <i>parC</i>, <i>gyrA</i>, <i>rpoB</i>) and virulence-associated genes (e.g., <i>prgB/asc10</i>, <i>cpsA/uppS</i>). Phylogenetic analysis indicated a close relationship with a human urinary tract isolate (ASM3679337v1). Mouse challenge experiments demonstrated that this strain induced significant intestinal histopathological damage. A subsequent transcriptomic analysis of infected tissues identified the differential activation of key signaling pathways, including NF-κB and MAPK. Our findings provide crucial insights into the resistance and pathogenic mechanisms of ruminant-derived <i>E. faecalis</i> and establish an experimental foundation for optimizing clinical antimicrobial therapy against such strains.