Integrated Phenotypic and Genomic Profiling of Antimicrobial Resistance and Virulence-Associated Determinants in Poultry-Derived Enterococcus spp. from Hungary

Background: Poultry-associated Enterococcus spp. are widespread commensals but may serve as One Health indicators when virulence-associated determinants and antimicrobial resistance co-occur. We characterized paired phenotypic and genomic profiles to delineate species-stratified virulome and resistome patterns. Methods: Isolates originated from a previously established poultry collection with MIC testing. Genotype–phenotype analyses were restricted to the whole-genome sequenced subset (n = 31). The acquired antimicrobial resistance genes were identified using the Comprehensive Antibiotic Resistance Database (CARD), and virulence-associated determinants were screened using the Virulence Factors Database (VFDB). Results were summarized as isolate-level presence/absence matrices and integrated with MIC-derived susceptible/intermediate/resistant categories. Results: The WGS subset comprised E. faecalis (n = 23) and E. faecium (n = 8) with diverse sequence types. Virulome architecture was strongly species-dependent: E. faecalis carried a broad repertoire of adhesion/biofilm-associated determinants, whereas E. faecium showed a limited set of high-confidence virulence-associated hits. Acquired resistance determinants were common across isolates, and resistome profiles displayed structured co-occurrence. Integrated analyses suggested only a modest overall association between virulence-gene burden and acquired resistome size, largely driven by species-level differences. Genotype–phenotype concordance was class-dependent, with incomplete alignment in several antimicrobial classes, consistent with mechanisms beyond the screened acquired gene set. The acquired resistance determinants detected in the WGS subset predominantly mapped to antimicrobial classes commonly used in food-producing animals (e.g., tetracyclines, macrolides, lincosamides, aminoglycosides, and phenicols), supporting interpretation in the context of production-associated antimicrobial selection rather than implying last-line clinical resistance by default. Conclusions: Poultry-derived enterococci may combine genetic features compatible with persistence/colonization and acquired antimicrobial resistance, with co-occurrence patterns shaped primarily by species/lineage background. These findings support risk-stratified One Health surveillance and targeted functional and mechanism-focused follow-up. This integrated virulome–resistome view highlights species-specific risk signatures in poultry-associated Enterococcus and identifies discordant high-level phenotypes that merit targeted mechanistic follow-up.