First Report of Food-Associated Enterococcus bulliens CFF05 from Thai Cooked Fermented Fish: Genomic Insights and Safety Assessment

Enterococci are frequently detected in fermented foods, where they contribute to product quality but may also raise food safety concerns due to antimicrobial resistance and virulence-associated traits. Enterococcus bulliens remains poorly characterized, with limited genomic data and no prior reports from fermented fish products. In this study, we isolated and comprehensively characterized E. bulliens strain CFF05 from Thai cooked fermented fish, representing the first food-associated genome of this species. Phenotypic analysis revealed resistance to ampicillin and clindamycin, intermediate susceptibility to erythromycin, and a β-hemolytic phenotype. Long-read sequencing produced a complete 2.24 Mb chromosome (38.4% GC; 2,581 coding sequences). Average nucleotide identity (99.4%) confirmed species assignment. Genomic screening identified vanW and vanY homologs, qacJ, and a hemolysin-associated gene (tlyA), while no plasmids or complete high-risk resistance operons were detected. Mobile genetic elements were predominantly chromosomal and associated with recombination and prophage regions rather than transferable determinants. Comparative pangenome analysis revealed strain-specific enrichment of amino acid, carbohydrate, and riboflavin biosynthesis pathways, suggesting adaptation to fermented fish environments. Although PathogenFinder predicted pathogenic potential, this signal was driven by conserved housekeeping genes. These findings highlight the importance of integrating phenotypic and genome-based analyses for safety assessment of food-associated enterococci.