LAUSR

Background The prevalence of antibiotic resistance genes (ARGs) in animal manure poses a threat to environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland and have the potential to cause outbreaks of bacterial resistance in agricultural environments. This study investigated the composition of ARGs in different animal manures and their derived organic fertilizers. Results The results showed that the abundance of several ARGs, such as sul 2, Tet B-01, Tet G-01 and Tet M-01, in organic fertilizer samples was 12–96% lower than that in animal manure. However, the abundance of Tet K and erm C was higher in animal manure than in organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, and antibiotics was observed by redundancy analysis (RDA). Procrustes analysis revealed a significant correlation between bacterial community structures and ARG abundance ( r  = 0.799, p  < 0.01). Nonmetric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additionally, the abundance of pathogenic bacteria (especially Actinomadura ) would increase rather than decrease in manure compared to organic fertilizer. Conclusion The diversity and abundance of most ARGs significantly decreased from animal manure to organic fertilizer. Microorganisms in the prepared organic fertilizer may mainly be inherited from the animal manure. The results also showed that the pathogens in the prepared organic fertilizer would significantly reduce, but would still cause partial pathogen proliferation.