Biological wastewater treatment plants (WWTP) have been under extensive scrutiny over their central role in the dissemination of antibiotic resistance genes (ARGs) of human origin. However, resistance gene expression, environmental selection, as well as mechanisms underpinning resistance exchange and dissemination among bacteria remain unknown. In the ResistFlow project we combine quantitative metatranscriptomes, metagenome assembly, amplicon sequencing, and qPCR to quantify the resistome in 12 Swiss WWTPs over four treatment stages: primary clarifier, nitrification, denitrification and secondary clarifier.
Overall, we find that wastewater and activated sludge bacterial communities harbored ∼108 to 1012 transcripts per liter derived from tens of thousands of ARGs that confer resistance to over 20 classes of antibiotics including five classes of last-resort antbiotics. We demonstrate that biological factors including horizontal gene transfer and bacterial community composition play a dominant role in shaping resistome structure, and provide evidence for the exchange of resistance gene between WWTPs and human pathogens, which highlights the clincial relevance of wastewater resistome. In addition, we showed that wastewater treatment greatly affects the resistome composition and selectively enriches certain types of antibiotic resistance genes in the clarified effluent.