Identification of Antibiotic Resistant Core Genes in the Greenhouse Soils of South Korea

Abstract

Antibiotic resistance genes (ARGs) have become a threat to global health and are ubiquitous in environmental settings as their reservoirs. Notably, agricultural activities influence on distribution of ARGs in the environment by various gene transfer system. This paper hypothesized that the greenhouse cultivation appears to contribute to the dissemination and proliferation of ARGs because of continuous input of manure, irrigation water, and fertilizer in its closed system. However, current risk assessment has focused on clinical settings, which are not proper in environmental settings, and there are various ARGs in environment. In South Korea, no other ARGs have been proposed as indicators in the context of growing greenhouse cultivation compared to other countries. Thus, we aimed at the determination of indicator genes in South Korea to alleviate the time and effort required for monitoring of antibiotic resistance. Forty-two greenhouse soil samples and nineteen control soil samples were analyzed in the aspect of abundance and distribution of 322 ARGs and 58 MGEs in order to exclude the interference possibility of soil types, ARGs inclination, and geographic difference for comprehensive analysis. In addition, the concentration of ions in soils along with pH and microbial community were investigated to figure out the difference between greenhouse soils and control soils. In this study, greenhouse soil showed a significantly high abundance of ARGs and high concentration of ions in soils compared to control soils. The taxonomic composition of microbial community between greenhouse soils and control soils was also different. Interestingly, the composition of core genes in the greenhouse soils and control soils was totally different and 24 core genes were selected from greenhouse soils. Among selected core genes, aadA5 and tetM, which are genes for aminoglycoside resistance and tetracycline resistance, respectively, were determined as indicators considering clinical relevance, the prevalence in soil resistome, association with MGEs, validation through pot experiment and correlation with abiotic and biotic factors. These results would contribute to continuous and rapid surveillance of antibiotic resistance dissemination and proliferation in the greenhouse, South Korea.