Understanding the Impact of Soil Health Practices on Antimicrobial Resistance

The long-term goal of this research is to identify practical and scalable solutions to reduce the onward transmission of pathogens and the genes that confer antimicrobial resistance. The goal of this proposal is to identify critical control points for the transmission of pathogens and AMR genes from ‘farm to table.’ Specifically, we focus on identifying soil management practices that reduce/increase the abundance and diversity of pathogens and AMR genes. Our approach combines field experiments, next-generation sequencing, and a suite of quantitative tools.

Goal 1. Characterize how soil management treatments shape microbial and antimicrobial resistance profiles. We will use whole genome sequencing to analyze samples from the farm, lagoon, soils, and crops.

Goal 2. Determine soil management practices that increase the abundance, diversity, and prevalence of pathogens and AMR. We will use structural equation modeling to quantify the relative contribution of different management practices on microbial communities. 

Goal 3. Identify specific management practices to reduce pathogens and AMR across the livestock-manure-soil-crop production chain. We will develop, evaluate, and refine epidemiological risk assessment analyses to quantify critical control points across the entire production system.