Application of pharmaceutical waste sludge compost alters the antibiotic resistome in soil under the Chinese cabbage system

Antibiotic resistance is a global threat posing risks to public health. China, as the largest consumer and producer of antibiotics, is generating a large amount of pharmaceutical waste sludge from the antibiotic manufacturing industry, which has the potential to be released into the environments by anthropogenic activities. Land application of pharmaceutical waste sludge compost (PWSC) is a popular way of PWSC disposal, with large amount of antibiotics might hence be introduced into the soil environments and result in the development of antibiotic resistance genes (ARGs). ARGs in PWSC amended soil-plant systems, their transmission routes and potential ecological risks are still unknown. A high-throughput qPCR chip was used to profile ARGs in Chinese cabbage (Shanghaiqing, Brassica chinensis L.) and soils (including phyllosphere, root endosphere, rhizosphere soil, and bulk soil) with PWSC amendment, aiming to study the effect of PWSC application on ARGs soil-plant systems. A total of 249 ARGs and 12 mobile genetic elements (MGEs) were detected in all collected samples. The highest number of detected ARGs was in the soil samples (up to 181) compared to the above and below-ground components of Chinese cabbage. Our results demonstrated the PWSC amendment increased the diversity and normalized abundance of ARGs in the amended soil-Chinese cabbage system. Mantel test and Procrustes analysis revealed the connection between ARG profiles and microbial communities (fungal and bacterial communities). Shared ARGs were identified among the Chinese cabbage phyllosphere, Chinese cabbage root, and rhizosphere soils, demonstrating a potential link between antibiotic resistome in Chinese cabbage and soils, with the amended soil as a key source of ARGs in the phyllosphere of Chinese cabbage. In summary, our findings provided novel evidence for a transmission route shared Zero-radius operational taxonomic units (ZOTUs) and ARGs were passed between the soil-Chinese cabbage system elements (i.e., amended soil, root, and phyllosphere) of ARGs from the PWSC amended soils to common green vegetables, highlighting a potential safety hazard of antibiotic resistome transfer from soils to the human food chain.