Antimicrobial resistance and virulence of Enterococcus faecium isolates from a traditionally fermented dairy beverage from Uganda

This study investigated antimicrobial resistance (AMR), virulence genes, and plasmid replicons in three Enterococcus faecium strains isolated from Bongo, a traditional fermented dairy beverage from Uganda. All three isolates showed extreme multidrug resistance, with minimum inhibitory concentrations at or above the highest levels tested for all 17 antibiotics. Whole genome sequencing revealed the presence of intrinsic AMR genes (aac(6’)-li, msrC), virulence-associated genes (acm, efaAfm), a stress-response gene (ClpL), and the repUS15 plasmid replicon linked to plasmid replication. These findings provide early evidence that fermented foods can serve as reservoirs of multidrug-resistant and potentially virulent E. faecium, highlighting a food safety concern and reinforcing the need for stricter control of food microbial contamination and more responsible antibiotic use in both human and veterinary settings, alongside broader surveillance.