Skip to main content
ARS Home » Research » Research Project #432319

Research Project: Characterizing Antimicrobial Resistance in Poultry Production Environments


Project Number: 6040-32000-010-000-D
Project Type: In-House Appropriated

Start Date: May 17, 2017
End Date: Jan 18, 2021

1. Characterize the antimicrobial resistance (including the resistome and mobilome) of pathogens and commensals from agroecosystems and identify factors that contribute to their spread. 2. Optimize methods for detecting bacteria with antimicrobial resistance and develop tools to assess biological and environmental factors that contribute to their persistence and transmission in agroecosystems.

Goals will be accomplished by identifying environmental factors associated with the persistence of resistance in microbial populations from poultry production environments (feces, litter, water and feed) that are under different management regimes (conventional, pastured and organic). Traditional and advanced molecular analyses will be used to characterize phenotypic and genotypic properties of populations including the resistome (i.e., the collection of all resistance genes in both pathogenic and non-pathogenic bacteria) and mobilome (genetic elements associated with transfer of antibiotic resistance (AR) genes between bacterial genera and species). Data to understand the effect of environmental factors on horizontal transmission of resistance genes between populations is urgently needed to inform risk assessment models and identify targets for mitigation studies. Research conducted as part of this project will evaluate the effect of nutrients, disinfectants and antibiotic concentrations on the rate of horizontal gene transmission by plasmids to pathogens like Salmonella enterica serovar Heidelberg and Enterococcus faecalis. Separate studies will investigate molecular properties of plasmids that are mobilized from the complex poultry litter microbiota to new bacterial recipients and the effect of environment on the rate of horizontal gene transfer. Quantitative data are needed to establish functional relationships between the persistence/growth of bacteria with antimicrobial resistance and management/environmental factors. To this end, methods will be optimized for sensitive, specific detection of AR targets in complex ecosystems and studies will be conducted to quantify (1) the effect of poultry litter re-use on the development and persistence of bacteria with antibiotic resistance and (2) to evaluate the effect of residual antibiotics and manure nutrients on the native soil AR microbiota and the manure-associated AR microbiota. Functional relationships will be established to describe the ecology of antimicrobial resistance under environmentally relevant conditions and to establish the effect of these management strategies and residual antibiotics on native and litter-associated microbial flora and on AR pathogens of importance to humans.