Estuarine sediments are key hotspots of intracellular and extracellular antibiotic resistance genes: A high-throughput analysis in Haihe Estuary in China

[Display omitted] •eARGs and iARGs were both diverse and abundant in Haihe Estuary sediments.•Multidrug resistance genes were both highly diverse and abundant in Haihe Estuary.•Salinity altered the composition and structure of bacterial community in estuary.•Bacterial community and MGEs were the major drivers of variation of ARGs in estuary. Estuaries lie between terrestrial/freshwater and marine ecosystems, receive considerable pollutant input from land-based sources, and are considerably influenced by human activities. However, little attention has been paid to combined research on extracellular antibiotic resistance genes (eARGs) and intracellular ARGs (iARGs) in the estuarine environment. In this study, we profiled eARGs and iARGs in sediments from Haihe Estuary, China by adopting high-throughput quantitative PCR and investigated their relationship with mobile genetic elements (MGEs), the bacterial community and environmental factors. The results showed that the abundance of eARGs ranged from 9.06 × 106 to 1.32 × 108 copies/g and that of iARGs ranged from 3.31 × 107 to 2.93 × 108 copies/g, indicating that estuarine sediments were key hotspots of eARGs and iARGs. Additionally, multidrug resistance genes were both highly diverse and abundant in Haihe Estuary, especially in coastal samples. The high abundance of vancomycin and carbapenemase resistance genes may pose a potential health risk to human. Salinity altered the composition and structure of the bacterial community. Partial redundancy analysis showed that the bacterial community and MGEs appeared to be the major drivers of ARG variance in estuarine sediment. This study provides an overview of the distribution of eARG and iARG along the Haihe Estuary and draws attention to the need to control pollutants in estuary ecosystems.