Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

• Distribution of ARGs in decentralized sewage facilities were investigated. • Bacitracin-ARGs were most predominant ARGs in rural wastewater. • ARGs were identified in bacterial and viral community. • ARGs of rpoB, drfE, gyrA and parC were both correlated with bacteria and phages. • More attention should be paid to the risk of spreading ARG by phages. The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG’s proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.