Metagenomic libraies from Waste Water treatment plant to investigate environmental AMR genes. UKCEH UKWiR WWTP metagenomes

The overall aim of this project was to better understand the role that wastewater treatment works (WwTWs) play in treating and transforming Antimicrobial Resistance (AMR) from raw influent to final effluents and sludges. The study included measurements of metals and antibiotics known to influence AMR as well as relevant information on the catchment and performance of the WwTWs involved. The study also aimed to characterise AMR across the different stages of wastewater treatment with the intention of identifying which processes influenced the final AMR presence in effluent. Approach Ten different WwTWs were sampled six times over the course of 11 months in 2020 and 2021. These WwTWs represented a range of secondary treatment processes, including trickling filters (TF), activated sludge (AS), integrated fixed film activated sludge (IFAS), as well as Biological Aerated Flooded Filter (BAFF) processes. Tertiary treatment processes included Nitrifying Submerged Aerated Filters (NSAF), lagoons, Filtabead, CoMag, Continuously Operated Upflow Filters (COUF), cloth filters and plastic High-Rate Flow media (HRF). Composite 24 h sampling was used for liquid samples and grab samples for the sludges. Samples were analysed for a range of parameters that were used to characterise AMR and the conditions that may favour or select for AMR during wastewater treatment. AMR was characterised to determine AMR prevalence and richness by culture-based analysis of non-resistant and cefotaxime-resistant Escherichia coli, quantitative-PCR (qPCR) of eight resistance, resistance-associated and microbial marker genes, metagenomics (DNA sequencing) of bulk liquid and sludge, and metagenomics of pooled E. coli culture samples. Contextual information included physicochemical parameters (nutrients, biochemical and chemical oxygen demand etc.) as well as measures of dissolved metals and a suite of 87 antibiotics and metabolites, measured using high resolution mass spectrometry.