Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing

Antibiotic resistance genes (ARGs) and virulence factors (VFs) pose considerable health risks to humans. The occurrence and abundance of several typical ARGs in the sea have been widely investigated. However, the full profiles and abundances of the antibiotic resistome and VFs in the South China Sea remain unexplored. Therefore, in this study, we investigated the full profiles of the ARGs and VFs, as well as their abundances and distribution, in the South China Sea using metagenomic approaches. In total, 140 ARG subtypes and 155 VFs were detected. The most abundant ARG was multidrug resistance gene, followed by bacitracin resistance gene. Flagella was the most abundant VF. Pearson correlation analysis revealed a strong and positive correlation between the abundances of ARGs and VFs. Redundancy analysis and co-occurrence network analysis showed that the predominant VFs were positively correlated with the predominant ARGs in the South China Sea. Nonmetric multidimensional scaling and Procrustes analyses demonstrated that the sampling sites were clustered into three compartments according to the geographical location, i.e., offshore, open sea, and reef zones. The abundances of ARGs and VFs in the offshore zone were much higher than those in the open sea and reef zones (p < 0.05). Several physico-chemical factors most closely associated with anthropogenic activities, i.e., nitrate, lead, copper, and zinc, were positively correlated with the predominant ARGs and VFs in the South China Sea. Our results suggest that the ocean is a large reservoir of diverse and abundant ARGs and VFs, which may threaten human health and seafood safety. These findings improve the understanding of the relationship between ARG dissemination and intensive anthropogenic activities and can aid in improving ocean management and seafood product safety.