Conjugative transfer of plasmid-borne antibiotic resistance genes to environmental bacteria in crop production systems irrigated with municipal wastewater effluents – CONTRA

Climate change is constraining the availability of water for irrigating crops in many parts of the world, threatening global food security. In response, the use of municipal wastewater effluent for irrigation is becoming a necessity. Wastewater effluent contains residues of antibiotics and other micropollutants, antibiotic resistant bacteria excreted by humans, and the antibiotic-resistance genes and mobile genetic elements that they carry. There is very little knowledge about what impact wastewater effluent might have on the reservoir of antimicrobial resistance in irrigated crop production systems. Likewise, what if any risk of transmission of antibiotic resistance genes from the effluent microbiome to the microbiome in the soil or on crops is largely unknown. This knowledge is required to identify if this practice will contribute to the transmission of antimicrobial resistance transmission from effluent back to to humans via the food chain or the environment. Should this be the case, the information gained would be used to inform policies and practices governing the acceptable quality of water used in various irrigation scenarios. The proposed research will characterize the complement of plasmids (the plasmidome) of municipal effluent. Long read metagenomic sequencing will be used to close plasmids, and provide genetic context for plasmid associated antibiotic resistance genes. Plasmid-host associations will be established using Hi-C approach. Associations between plasmid composition and community structure will be searched using machine learning. In vitro, the presence of quite low antibiotic concentrations can increase the frequency of conjugation. This will be explored in soil and in phyllosphere communities. The Hong Kong group will contribute extensive experience with bioinformatics tools deployed on long read and metagenomic sequencing. The France group will undertake experiments with irrigation on crops, and has extensive experience in bacteriology.