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The proposed research will provide a novel systems-based approach to characterize and quantify the presence of genes associated with antibiotic resistance in the environment. The proposed Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), will enable the identification, quantification, and surveillance of antibiotic resistant genes (ARGs) in the environment. By demonstrating this approach in both laboratory model systems and the field, we hope to identify critical control points that may be sensitive to the mitigation of emergence, spread, and persistence of resistance in the environment. The data collection enabled by DARTE-QM can be integrated into biological risk assessments that will inform policies toward the successful management of resistance. The key objectives of this research are as follows: Development of DARTE-QM to characterize diverse ARGsEvaluation of DARTE-QM to monitor ARGs in environmental samples "from rump to runoff" (e.g., manure, soil, sediment, and water samples).Evaluation of DARTE-QM to characterize fate and transport ARGs released in environment from animal manure in soil column experiments integration of DARTE-QM tools, data, and associated analysis with training, education, and outreach to be adapted by diverse users and stakeholders
The global spread of antimicrobial-resistant (AMR) organisms and spread of AMR-associated genes poses a serious threat to the safety of our food and public health while being responsible for increased hospitalization and mortality of both humans and production animals. The release of AMR genes and organisms, specifically antibiotic resistant genes (ARGs) and microbes, into the environment from agricultural sources is considered a serious threat, but little is known about their persistence and spread in the environment. Current risk assessment models cannot adequately characterize and quantify the proliferation of antibiotic resistance, especially in non-clinical settings. Reliable measurement and surveillance of antibiotic resistance is a complex problem that requires innovative solutions. This research develops novel technology that will generate quantitative data on antibiotic-resistance genes in environmental samples. The advantages of this approach over existing technologies are that it does not require the cultivability of environmental bacteria; hundreds of resistance genes can be detected simultaneously; and hundreds of samples can be tested simultaneously. Applying this technology to environmental samples will determine points of maximum resistance gene diversity, thereby identifying the most efficacious mitigation points along the food chain. The development of this transformative approach that we are calling DARTE-QM (Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring) integrates high throughput DNA sequencing technologies and an open-access data analysis pipeline that can identify the microrganisms in environmental samples that are contributing to antibiotic resistance gene prevalence. Our long-term vision is that we develop a technological platform that can be used to target ARGs for any environmental study and is scalable, accessible, and affordable to include in every microbial monitoring program.