Mobile genetic elements are the Major driver of High antibiotic resistance genes abundance in the Upper reaches of huaihe River Basin

Highlights

• ARGs pollution level in the tributaries was heavier than that in the mainstream.

• Tributaries could pose impact on mainstreams in ARGs abundance.

• The abundance of vancomycin and carbapenems-ARGs are high.

• MGEs are the major driver of ARGs shift in Huaihe river basin.

Abstract

Rivers are considered a vital reservoir of antibiotic resistance genes (ARGs) and are critical to disseminate ARGs. The present study delved into the ARGs pollution of the sediments in the upper reaches of Huaihe river, one of the seven longest rivers in China, by high-throughput quantitative PCR. Subsequently, the relationship between ARGs and the bacterial community/mobile genetic elements (MGEs) was determined. As revealed from the results, the overall ARGs ranged from 2.65×10⁻³ to 6.14×10^-2/16S copies, and the abundance of ARGs in the tributaries was significantly higher than that in the mainstreams (p<0.05). Moreover, the ARGs introduced by tributaries were capable of affecting the whole mainstream of Huaihe river. As suggested from the results of co-occurrence analysis and pRDA analysis, MGEs were reported as the major driver to disseminate ARGs in the upper reaches of Huaihe river basin. The larger the MGEs proportion, the higher the likelihood of ARGs transferring from antibiotic resistance bacteria to human pathogens in Huaihe river.

Introduction

Over the past few years, misuse of antibiotics led to rapid an up-regulation of antibiotic resistance genes (ARGs) (Zhang et al., 2020). ARGs are capable of transferring among bacterial species via horizontal gene transfer (HGT), so they distribute widely in the environment (Zhang et al., 2019; Ding et al., 2016). Human activity is considered one of the major reasons causing the ubiquitous pollution of ARGs in the environment (Allen et al., 2010). Existing studies have recently analyzed the correlation of human gut-specific bacteria or bacteriophage (e.g., crAssphage) with the antibiotic resistance gene abundances under anthropogenic impacts (Chen et al., 2019a, 2019b, Karkman et al., 2019; Stange et al., 2019; Chen et al., 2020). The ARGs in the environment can transfer to human or animal pathogens, and environment can constantly threaten human and animal health by ARGs (Niu et al., 2016).

Water refers to the most extensively distributed medium worldwide, capable of spreading the pollutants worldwide (Chow et al., 2015; Manaia et al., 2016; Suzuki et al., 2017; Quintela-Baluja et al., 2019). Accordingly, aquatic environment is considered a vital reservoir of ARGs. Rivers, one of the critical aquatic environments, arouse most of the attention for the high capacity in ARGs transportation (Qiao et al., 2018; Singh et al., 2019; Xu et al., 2015). A system of river basin consists of a mainstream and tributaries, and considerable interactions exist in the identical system. Thus, ARGs should be quantified at basin level to comprehensively determine the ARGs pollution level in a river. Moreover, mobile genetic elements (MGEs) can facilitate ARGs to propagate (Allen et al., 2010; Yao et al., 2020). Besides, the results of recent studies indicated that bacteria community is the major driver of ARGs (Jia et al., 2015, 2017; Zhou et al., 2017), and further researches should be conducted to verify the role of MGEs and bacteria community in various environmental media.

Huaihe river, originating from Tongbai Mountain in Henan, refers to one of the seven longest rivers in China. The overall length is approximately 1000 km, and the drainage area of the river is nearly 27,000 km². Its annual average amount of surface water resources reaches 85.4 billion m³, and it is the source of the agricultural and drinking water in the basin. The booming of economy and urbanization has caused heavy pollution in this river. It has been reported that the water quality was lower than Grade IV in over 50 % of the rivers, by complying with the National Surface Water Quality Standards in China since 1980s (Wang et al., 2014). Investigations of different pollutants (e.g., heavy metal), PAHs and organochlorine pesticides were performed both in water and sediments of this river (Liu et al., 2016; Lu et al., 2015b; Luo et al., 2016). However, the polluting characteristic of ARGs in this river basin remains unclear. Studies on ARGs in the upper reach are critical to gain insights into its contribution to the pollution in the middle and lower reaches.

The abundance of 96 genes (87 ARGs, 2 class I integron-integrase genes, 6 transposase genes and 16S rRNA gene) in 17 DNA samples was investigated with high throughput-quantitative PCR (HT-qPCR). By Illumina 16S rRNA gene sequencing, the bacterial community was analyzed. Sediments were taken as the target medium since they are capable of reflecting the long-term pollution status and easy to incubate for ARGs analysis (Yang et al., 2017b). The objectives of the present study included: 1) to determine the spatial distribution pattern of ARGs in the sediments from the upper reach of Huaihe river; 2) to characterize the bacterial community of the river; 3) to address the major factors contributing to the ARGs shift in sediments of Huaihe river.