THE SCOOP ON POOP: CONNECTING MANURE MANAGEMENT TO ANTIMICROBIAL RESISTANCE

<b>Project Methods</b><br> Objective 1: To address the question of the impacts of antibiotic usage and pressures in animal production, we propose to characterize the AMR response in manures from swine with and without previous antibiotic usage histories. Our hypothesis is that decreased AMR will be observed in manures associated with animals without antibiotic usage, but that this will vary based on the type and duration of antibiotic exposure. Further, we hypothesize that the selection of resistant strains and the emergence of AMR to antibiotic pressure is predictable. We will primarily implement laboratory experiments to address these questions, due to the ability to standardize manures and control environmental conditions for comparable results; however, to further broaden the impact of these results, we will also collect manure samples from across Iowa State to identify if indicators of AMR are present under varying management conditions and animal sources.Objective 2: The success of using bacterial indicators for AMR is directly linked to their representation of risks within the system of interest. For example, for well-studied foodborne pathogens, such as Enterobacteriaceae, and in relatively low complexity environments (e.g., food surfaces), it is possible to use known AMR genes to predict a resistant phenotype. However, the diversity of AMR determinants and resistant phenotypes in environmental samples, such as soils and manures, often lead to inconsistencies between the presence of genes and phenotypic expression of resistance. These discordances are very likely due to the lack of data on bacterial species and their underlying mechanisms of emerging resistance. To better understand the response of traditional and novel indicator organisms, in this objective, we will characterize the AMR gene determinants, phenotypes, and antibiotics during manure storage.Objective 3: Based on conversations with stakeholders, we have also chosen to evaluate mitigation alternatives that are being considered by other stakeholders that have also shown promise in our previous experiments. These treatments include anaerobic digestion, which is receiving increased interest due to renewable fuel standards; aeration, which is receiving attention as an odor control practice; solid liquid separation which is an odor control practice; and liming which is a chemical treatment used for cases where pathogen reduction is required.Objective 4:This proposal will develop indicators of AMR based on both our previous characterization of swine manure and the laboratory experiments proposed in this study. In order to increase the reliability of these indicators, we would like to show that they are broadly representative and present in diverse manures, beyond swine manure.