Background: Microbiota carrying multiple antibiotic resistance genes (ARGs) and virulence factors (VFs) are posing increasing risks to public health. Particularly the rapid spread of human pathogenic bacteria (HPB) with antibiotic resistance is recognized as a top health issue. The occurrence and abundance of ARGs in aquaculture have been investigated following metagenomic approaches. However, few studies have investigated the antibiotic resistome and VFs and their HPB hosts in aquaculture. Moreover, the relationships between ARGs and VFs and their microbiome in aquaculture are poorly understood. Results: The profiles of the antibiotic resistome, VFs, and HPB in aquaculture in Southern China were investigated. In total, 492 subtypes of 24 ARGs types were detected. Multidrug ARGs were most predominant, followed by macrolide-lincosamide-streptogramin (MLS). Proteobacteria were the most predominant phylum carrying ARGs, followed by Firmicutes. Fifty-two HPB genera were detected. Firmicutes was the most abundant phylum, followed by Proteobacteria. Staphylococcus was the most abundant HPB genus. The samples contained 363 VFs, with Capsule being the most abundant. Seven HPB phyla, including 42 HPB genera, carried VFs, and the abundance of Bacillus was highest. The abundances of ARGs and VFs were highest in the sediment. However, the abundance of HPB was highest in shrimp guts and Staphylococcus was most abundant. Most ARGs were more prevalent on chromosomes than on plasmids. Source tracking analysis showed that the sediment was the greatest contributor to microbes carrying ARGs, VFs, and HPB in shrimp guts. Additionally, the water source contributed some of the HPB of shrimp guts. Conclusions: This study provides in-depth profiles of the abundances, diversity, distribution, and prevalence of ARGs, VFs, and their hosts HPB in aquaculture for the first time. Sediment was the most direct and important contributor to the ARGs, VFs, and HPB in the shrimp guts. The prevalence of HPB in aquaculture, particularly the high abundance of Staphylococcus in shrimp guts, poses potential risks to human health and food safety. Aquaculture water sources should be monitored and protected. The findings of this study provide a better understanding of the dissemination and hosts of ARGs and VFs for improving aquaculture management and public health surveillance.
