Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment

Authors: BHATTACHARJEE, ANANDA - University Of California, Riverside; PHAN, DUC - University Of California, Riverside; ZHENG, C - University Of California, Riverside; Ashworth, Daniel; Schmidt, Michael - Mike; MEN, YUJIE - University Of California, Riverside; Ferreira, Jorge; MUIR, G - Ezbiome; HASAN, N - Ezbiome; Ibekwe, Abasiofiok - Mark

Submitted to: Environmental International
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2024
Publication Date: 5/18/2024
Citation: Bhattacharjee, A.S., Phan, D., Zheng, C., Ashworth, D.J., Schmidt, M.P., Men, Y., Ferreira, J.F., Muir, G., Hasan, N., Ibekwe, A.M. 2024. Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment. Environmental International. 183. Article 108374. https://doi.org/10.1016/j.envint.2023.108374.
DOI: https://doi.org/10.1016/j.envint.2023.108374

Interpretive Summary: Antibiotics are vital for modern healthcare, combating bacterial infections and saving lives. However, the widespread use of antibiotics has resulted in large amounts of their residues in municipal wastewater. Antibiotics enter the sewage system through multiple sources such as the excretion of urine and feces of human and domestic animals, improper disposal of unused/expired drugs, waste streams from hospitals, and the production of antibiotics. However, there are major concerns regarding chemicals of emerging concern such as antibiotics and antibiotic resistance genes in treated municipal wastewater. In this study, we investigated the bacterial composition and resistance genes in the soil–plant–earthworm continuum after irrigation of spinach and radish with treated wastewater containing different antibiotics. This study revealed that a total of 271 antibiotics resistance genes and 9 mobile genetic elements were detected in all samples. Higher diversity and abundance of antibiotics resistance genes were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. Our results show that microbial diversity in spinach and radish phyllosphere were lower than those from the bulk soil, rhizosphere soil, and earthworm feces. However, the number of antibiotic resistance genes and antibiotic resistant bacteria enriched in spinach was higher than that of radish. The results of this research will be used by researchers and agencies that are involved in wastewater management.

Technical Abstract: Antimicrobial resistance (AMR) spread in agricultural systems through irrigation water is a serious public health issue and can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the microbiome and resistome in the soil–plant–earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in phase I. The 16S data indicated that the rhizosphere microbial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to radish, spinach showed more susceptibility to changes in ARG dynamics in the soil biome. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Earthworm fecal samples and their corresponding soil environments showed different ARG dynamics structures, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings provide an insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water and provides additional helpful understanding of the potential human health risks associated with ARGs.