TY - JOUR T1 - Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods JF - bioRxiv DO - 10.1101/2022.04.22.489054 SP - 2022.04.22.489054 AU - Andrea Ottesen AU - Brandon Kocurek AU - Padmini Ramachandran AU - Elizabeth Reed AU - Seth Commichaux AU - Gunnar Engelbach AU - Mark Mammel AU - Sanchez Saint Fleurant AU - Shaohua Zhao AU - Claudine Kabera AU - Amy Merrill AU - Nathalie Bonin AU - Hannah Worley AU - Noelle Noyes AU - Christina Boucher AU - Patrick McDermott AU - Errol Strain Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/04/25/2022.04.22.489054.abstract N2 - Surface waters present a unique challenge for the monitoring of critically important antimicrobial resistance. Metagenomic approaches provide unbiased descriptions of taxonomy and antimicrobial resistance genes in many environments, but for surface water, culture independent data is insufficient to describe critically important resistance. To address this challenge and expand resistome reporting capacity of antimicrobial resistance in surface waters, we apply metagenomic and quasimetagenomic (enriched microbiome) data to examine and contrast water from two sites, a creek near a hospital, and a reservoir used for recreation and municipal water. Approximately 30% of the National Antimicrobial Resistance Monitoring System’s critically important resistance gene targets were identified in enriched data contrasted to only 1% in culture independent data. Four different analytical approaches consistently reported substantially more antimicrobial resistance genes in quasimetagenomic data compared to culture independent data across most classes of antimicrobial resistance. Statistically significant differential fold changes (p<0.05) of resistance determinants were used to infer microbiological differences in the waters. Important pathogens associated with critical antimicrobial resistance were described for each water source. While the single time-point for only two sites represents a small pilot project, the successful reporting of critically important resistance determinants is proof of concept that the quasimetagenomic approach is robust and can be expanded to multiple sites and timepoints for national and global monitoring and surveillance of antimicrobial resistance in surface waters.Competing Interest StatementThe authors have declared no competing interest. ER -