Skip to main content
ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Bacterial Epidemiology & Antimicrobial Resistance Research » Research » Research Project #433649

Research Project: The HARVEST Initiative: On Farm Environmental Sampling for Organic Small Farms

Location: Bacterial Epidemiology & Antimicrobial Resistance Research

Project Number: 6040-32000-010-007-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Oct 1, 2017
End Date: Sep 30, 2018

Demand for poultry and other agricultural products produced using alternative management practices is increasing. Within the U.S., organic food sales increased 4-fold between 2000 and 2010 and does not take into account other alternatively grown (e.g. all-natural, freerange, pastured) poultry products that are increasing in prevalence; therefore the overall influence of these alternatively grown poultry products may be greater than realized. Failure to address the gap in research addressing microbial safety of these products may result in preventable illnesses and setbacks in meeting goals of regulatory agencies to reduce food borne illness by 2020. The use of small, multi-commodity, AGP-free farms for sampling to permit methods evaluation, epidemiologic tracking of pathogens on farm, and microbiome analysis (to evaluate antimicrobial resistance genes (resistome), mobile genetic elements associated with movement of important gene targets (mobilome)) will help to provide a baseline census for media comparison and microbial communities, document the dynamics of known pathogens and associated antimicrobial resistance patters, identify emerging pathogens, and help evaluate specific interventions to improve animal and subsequently human health with respect to these emerging consumer products. Therefore the purpose of this project is to isolate foodborne pathogens and perform metagenomics analysis on these pathogens, resistome and mobilome present in environmental samples (USDA certified organic produce, soil, irrigation water, compost, and biological soil amendments of animal origin) from USDA organic farms in North East Georgia. This work will elucidate the risks of compost and biological soil amendments of animal origin use and the connection between these amendments and pathogen presence on produce ready for the consumer. Additional data that will be generated by this work include determining whether nutrient and heavy metals present in soil amendments and soils contribute to the pervasiveness of pathogenic bacteria growth and whether antibiotic resistant strains of pathogenic bacteria are maintained on farmers’ market produce.

Both the Agricultural Research Service (ARS) and University of Georgia (UGA) collaborators maintain previously established relationships with several, small, organic (or transitioning) farms that serve three local farmer’s markets (including one market that specifically targets under-served populations). The participating farms are defined as small with respect to coverage by regulatory requirements and other guidelines (USDA-FSIS, 2006; FDA 2009-2010). Initial assessments demonstrated that these producers use alternative produce productions, animal husbandry, and processing practices compared to larger conventional operations. Producers agreed to complete a questionnaire (currently in development) regarding overall farm management practices. Additionally, the producers allow frequent and consistent on-farm sampling of growing poultry, produce, soil, irrigation water, fertilizer, compost and fecal samples from any additional agricultural animals on these farms. This data will directly address risk assessment needs associated with the use of biological solid amendments of animal origin (BSAOO). Poultry, compost, and produce samples originating from the participating farms will be collected thrice during the growing season. Sample origin will be double-blinded. On-farm and farmers market source samples will be tested for zoonotic, food-borne pathogens including Listeria monocytogenes, Salmonella, E. coli, and Campylobacter spp. All recovered pathogens will be further sub-typed and subjected to antimicrobial sensitivity testing (AST).