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Engineering >> 2022, Volume 15, Issue 8 doi: 10.1016/j.eng.2022.05.011

Three-Year Consecutive Field Application of Erythromycin Fermentation Residue Following Hydrothermal Treatment: Cumulative Effect on Soil Antibiotic Resistance Genes

a State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
b University of Chinese Academy of Sciences, Beijing 100049, China
c State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
d Institute for Biomedicine & the Centre for Antibiotic Resistance Research, University of Gothenburg, Göteborg, SE-413 46, Sweden
e Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia

Received:2021-12-15 Revised:2022-04-23 Accepted: 2022-05-24 Available online:2022-06-11

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Fermentation-based antibiotic production results in abundant nutrient-rich fermentation residue with high potential for recycling, but the high antibiotic residual concentration restricts its usefulness (e.g., in land application as organic fertilizer). In this study, an industrial-scale hydrothermal facility for the treatment of erythromycin fermentation residue (EFR) was investigated, and the potential risk of the long-term soil application of treated EFR promoting environmental antibiotic resistance development was evaluated. The treatment effectively removed bacteria and their DNA, and an erythromycin removal ratio of up to approximately 98% was achieved. The treated EFR was utilized as organic fertilizer for consecutive field applications from 2018 to 2020, with dosages ranging from 3750 to 15 000 kg∙hm-2, resulting in sub-inhibitory levels of erythromycin (ranging from 0.83–76.00 μg∙kg-1) in soils. Metagenomic shotgun sequencing was then used to characterize the antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial community composition of the soils. The soil ARG abundance and diversity did not respond to the treated EFR application in the first year, but gradually changed in the second and third year of application. The highest fold change in relative abundance of macrolide-lincosamidestreptogramin (MLS) and total ARGs were 12.59 and 2.75 times, compared with the control (CK; without application), respectively. The soil MGEs and taxonomic composition showed similar temporal trends to those of the ARGs, and appeared to assist in driving increasing ARG proliferation, as revealed by correlation analysis and structural equation models (SEMs). The relative abundance of particular erm resistance genes (RNA methyltransferase genes) increased significantly in the third year of treated EFR application. The close association of erm with MGEs suggested that horizontal gene transfer played a critical role in the observed erm gene enrichment. Metagenomic binning results demonstrated that the proliferation of mac gene-carrying hosts was responsible for the increased abundance of mac genes (efflux pump genes). This study shows that sub-inhibitory levels of erythromycin in soils had a cumulative effect on soil ARGs over time and emphasizes the importance of long-term monitoring for assessing the risk of soil amendment with treated industrial waste.

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