Effects of hygiene methods on the microbiome and resistome of poultry litter

Abstract The inappropriate use of antibiotics in poultry farming and the presence of antibiotic residues in the environment significantly impact the development of resistance among microorganisms present in the production ecosystem. The environment of the henhouse, including chicken manure, creates excellent conditions for the spread of antibiotic-resistant bacteria (ARBs). The presence of ARBs in the litter often leads to the transfer of antibiotic resistance genes (ARGs) through horizontal gene transfer (HGT). Considering the risks associated with the agricultural use of manure, all sanitation treatments applied to poultry litter before its agricultural use should effectively eliminate physicochemical (antibiotic residues, heavy metals) and microbiological (ARBs, ARGs) hazards. This review aims to analyse the current practices in rational manure management, aligned with bio-economy principles, and evaluate their effectiveness in reducing the spread of antibiotic resistance and pathogens in the poultry production ecosystem. This review considered biological, chemical and physical processes for poultry litter treatment applicable in livestock settings, including the use of biopreparations, humic substances, and aluminosilicates during chicken rearing. Post-rearing methods such as the application of organic additives, minerals (calcium compounds), and silver-based nano preparations are also discussed, along with biological and physical methods such as storage, anaerobic digestion, composting and pasteurisation.