Antimicrobial resistance, virulence profiles, and host metabolic associations of Enterococcus spp. in the gut of wild giant pandas (Ailuropoda melanoleuca)

The giant panda (*Ailuropoda melanoleuca*), an endangered Chinese endemic species, is threatened by intestinal diseases from pathogenic bacteria. Gut‑resident *Enterococcus* can act as opportunistic pathogens, with risks stemming from antimicrobial resistance and virulence gene spread. Here, 28 *Enterococcus* strains were isolated from faeces of wild giant pandas in Tangjiahe National Nature Reserve. Combining whole‑genome sequencing, antimicrobial susceptibility assays and untargeted metabolomics, we characterized resistance and virulence profiles and their links to host metabolites based on limited isolates. Four representative strains harboured abundant resistance and virulence genes (57‑69 per strain), yet remained phenotypically susceptible to key therapeutic antimicrobials, indicating a “genetic reservoir‑susceptible phenotype‑environmental trace” resistance pattern. Fecal metabolomics identified lipids and amino‑acid derivatives as major metabolites, alongside tentatively annotated fluoroquinolone‑related features suggestive of low‑level environmental exposure. Mantel tests showed metabolite‑virulence gene associations, e.g., amino acids/lipids correlated positively with *scm* and negatively with capsule‑synthesis genes, whereas short‑chain fatty acids and bile acids correlated with *bopD*. This work highlights the value of multi‑omics surveillance for evaluating wildlife antimicrobial resistance and generates hypotheses for gut opportunistic pathogen research.