Species-aware interpretation of vancomycin-related genomic signals in poultry-derived Enterococcus spp.: a confirmatory phenotyping and whole-genome sequencing framework for One Health surveillance.

BACKGROUND: Poultry-associated enterococci are relevant to One Health surveillance, yet interpreting vancomycin-related genomic signals requires careful consideration of species biology and detection confidence. METHODS: We analyzed broth microdilution MIC data for 218 poultry-origin Enterococcus isolates from an archival strain bank in Hungary and paired these data with whole-genome sequencing (WGS) for 73 isolates with linked MIC records. Vancomycin MICs for isolates previously flagged as showing elevated vancomycin MICs and/or phenotype-genotype discordant profiles were re-tested in three parallel confirmatory broth microdilution measurements using single-colony subcultures, and final confirmed MIC values are reported. RESULTS: In the final dataset, no confirmed vancomycin MIC value exceeded 4 μg/ml. Resistome screening of the 73 genomes (CARD-based output) yielded 1,448 resistance-associated annotations (181 unique gene calls; median 12 per genome) and did not detect canonical acquired van operons consistent with vanA, vanB, vanD, vanM, or vanN. van-associated signals were limited to vanC-like components, vanG-type regulatory elements (vanRG and/or vanSG), and a single vanW-annotated record, highlighting the need for species-aware interpretation and locus-level validation. CONCLUSIONS: These results support a surveillance-grade workflow that anchors van-related genomic reporting to confirmatory phenotyping, genome-confirmed species assignment, and confidence-aware locus inspection to minimize false alarms and improve One Health interpretability.