A comprehensive study of the microbiome and resistome of chicken waste from intensive farms

Abstract

The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic resistance genes (ARG) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry to the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARG, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed by high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.