Comparative analysis of wastewater sample processing methods for antimicrobial resistance surveillance

Antimicrobial resistance monitoring in wastewater represents a key challenge, especially in light of the multiple methods available. Our study assessed the impact of selected sample processing techniques on microbial diversity and antimicrobial resistance gene recovery from wastewater. We analyzed 38 subsamples derived from 12 wastewater samples collected across three wastewater treatment plants over 4 months. We compared the effects of different centrifugation volumes (50, 250 mL), speeds (3,400 × g vs 15,000 × g), and pellet versus filter concentration methods, as well as the performance of two DNA extraction kits-DNeasy PowerSoil Pro Kit and DNeasy PowerLyzer Kit (Qiagen, DE)-on wastewater samples. Additionally, we compared the performance of two DNA quantification instruments, NanoDrop One and Invitrogen Qubit 4 (Thermo Scientific, US). The analysis involved 16S rRNA gene sequencing on an Illumina MiSeq platform (PE250, 10M reads) and quantitative PCR (qPCR) of 11 selected antimicrobial resistance genes (ARGs). Higher centrifugation speeds and larger sample volumes lead to improved DNA yield. Pellets generally exhibited higher (1.32 times) ARG recoveries compared to filters. DNA quantification methods showed strong positive correlation (Pearson R = 0.78, Spearman ρ = 0.81, P < 0.01) with each other and with qPCR data. The approach implemented in this study (centrifuging 200 mL samples at 15,000 × g, followed by extraction with the DNeasy PowerSoil Pro Kit) shows promise for antimicrobial resistance (AMR) monitoring.

To monitor the prevalence of antimicrobial resistance genes (ARGs) is crucial for anticipating and mitigating the spread of antimicrobial resistance (AMR). Urban wastewater provides community-level data to inform timely interventions. By establishing a method that balances efficiency and feasibility, this protocol represents a step toward a standardized wastewater surveillance (WS) framework for AMR, enhancing our ability to safeguard community health.