Occurrence and antimicrobial resistance profiles of enterobacteria in treated poultry manure and agricultural soils in Uruguay

Land application of poultry production manure requires safe management strategies to evaluate and mitigate the dissemination of antimicrobial-resistant bacteria and opportunistic pathogens into agroecosystems This study evaluated the presence of zoonotic pathogens and their antimicrobial resistance profiles in poultry manure before and after composting, anaerobic digestion, and Quick Wash treatments, as well as in soils fertilized with these amendments. All samples were processed through bacterial isolation, molecular identification, and susceptibility testing against 17 antibiotics. A total of 106 isolates were collected and screened. Enterobacteria predominated (98.6 %), mainly Klebsiella spp. and E. coli. Among 37 E. coli isolates, virulence genes compatible with EPEC were identified in three isolates, and other virulence factors in four additional isolates. Antibiotic resistance was observed across all isolates from treated manure and soil, particularly against β-lactams, quinolones, aminoglycosides, and fosfomycin. Twelve multidrug-resistant isolates were identified, mainly Klebsiella spp., Enterobacter spp., and E. coli, with resistance associated with AmpC β-lactamases. None of mcr-1, mcr-2, mcr-5 and mcr-9 genes for colistin resistance, were detected. These findings demonstrate the presence of antibiotic-resistant enterobacteria in soils and poultry manure and also it’s persistence in poultry manure after physical, chemical and biological treatments. The presence of antibiotic-resistant enterobacteria highlights the need for monitoring and mitigation strategies to control the environmental spread of antimicrobial resistance.