Phenotypic Characterization and Antibiotic Resistance Profiles of Pathogenic Bacteria Isolated During Anaerobic Digestion of Pig Slurry

Antimicrobial resistance (AMR) represents a growing global health threat, with livestock effluents serving as significant reservoirs of antibiotic-resistant bacteria. This study evaluated the effectiveness of mesophilic anaerobic digestion (AD) in reducing pathogenic bacteria and AMR in pig slurry. Twenty-four samples were collected from two pilot-scale biodigesters (800 L, 56-day hydraulic retention time, ambient temperature) installed in Abidjan, Côte d'Ivoire. Bacterial identification was performed using MALDI-TOF MS, and antimicrobial susceptibility testing was conducted using the disk diffusion method according to CASFM 2023 guidelines. A total of 103 isolates belonging to 13 pathogenic species were identified. Firmicutes (Bacillus, Clostridium, Staphylococcus, and Enterococcus) dominated with 52.4% of isolates, followed by Proteobacteria (47.6%). AD significantly altered microbial composition (p < 0.05), achieving 3-5 log₁₀ CFU g⁻¹ reductions for Escherichia coli, Enterococcus, and Salmonella. However, spore-forming bacteria (Bacillus, Clostridium) persisted throughout the process. Antimicrobial susceptibility testing revealed high resistance rates: Gram-positive cocci showed 64% resistance for Enterococcus (MAR index 0.64), Enterobacteriaceae 52% (MAR 0.52), and Pseudomonas 51% (MAR 0.51). Yersinia enterocolitica was the most abundant species isolated (17.5% of total isolates). While mesophilic AD effectively reduces microbial loads, it does not ensure complete elimination of antibiotic-resistant pathogens. Complementary post-treatment processes are necessary before agricultural valorization of digestates to prevent environmental dissemination of AMR.