Antibacterial effects of probiotic fermented shallot and garlic chive extracts against multidrug-resistant Proteus mirabilis and Escherichia coli in a chicken model

Escherichia coli and Proteus mirabilis are significant Gram-negative pathogens causing disease and widespread antibiotic resistance in chickens. The development of natural alternatives to antibiotics is crucial for sustainable poultry production. This study evaluated the antibacterial effects of extracts from shallots and garlic chive, fermented by probiotic bacteria, against pathogenic isolates from chickens. Bacterial isolates from 35 chicken fecal samples were identified, and their pathogenicity was assessed in vivo. Pathogenic strains were confirmed by 16 S rRNA sequencing and screened for virulence genes (Stx1, ZapA) and antibiotic resistance. Extracts from shallots and garlic chive were fermented using Lactobacillus plantarum 1582 and Bacillus subtilis BSn5. Minimum inhibitory (MIC) and minimum bactericidal (MBC) concentrations of the extracts were determined against the pathogenic isolates. From the samples, 18 Proteus spp. and 21 E. coli isolates were identified. Five P. mirabilis (27.8%) and four E. coli (19.0%) isolates were pathogenic, with all pathogenic E. coli harboring the Stx1 gene. All isolates were multidrug-resistant. The fermented extracts showed strong activity, particularly against P. mirabilis (MIC: 0.98–3.92 mg/mL; MBC: 1.95–7.82 mg/mL). The activity against E. coli was also notable (MIC: 0.98–126 mg/mL; MBC: 3.92–250 mg/mL). Fermented garlic chive extract was more potent, which correlated with its higher allicin and total flavonoid content. Fermented extracts of shallot and garlic chive demonstrate significant antibacterial activity against multidrug-resistant P. mirabilis and E. coli. These findings highlight their potential as effective natural antibiotic alternatives for use in the poultry industry.