Table to farm: Using shotgun metagenomics to quantify antibiotic resistance on farms feeding food scraps to laying hens

Project Overview

Project Type: Graduate Student
Funds awarded in 2016: $14,909.00
Projected End Date: 12/31/2017
Grant Recipient: University of Vermont
Region: Northeast
State: Vermont
Graduate Student:
Faculty Advisor:
John Barlow
University of Vermont

Annual Reports


  • Animals: poultry


  • Animal Production: animal protection and health
  • Crop Production: food product quality/safety
  • Education and Training: on-farm/ranch research
  • Soil Management: composting
  • Sustainable Communities: local and regional food systems, sustainability measures

    Proposal abstract:

    The objective of this project is to establish a methodology for a novel antibiotic resistance screening tool and use this technology to directly benefit farmers feeding food scraps to poultry. Diversion of food scraps for agricultural use is a key component of the US EPA Food Recovery Hierarchy, and is present on farms in Vermont and across the U.S. While these diverted products are a sustainable feed source, they have the potential to carry novel microorganisms and associated antimicrobial resistance to farms, making their safety status unknown and posing a potential risk to both poultry and farmer livelihood. This project will address this risk by screening for and categorizing antimicrobial resistance genes (ARGs) in post-consumer food scraps and other off-farm materials entering Vermont composting facilities with integrated poultry production. The proposed project is novel and timely as many states have recently passed legislation similar to Vermont’s Act 148: Universal Recycling and Composting Law and aligns with the current U.S. priorities to address the growing problem of antimicrobial resistance in agriculture. By understanding the presence and background of ARGs in post-consumer food scraps, scientists and farmers will have insight into the safety and true value of these feeding programs. Our long-term goal is to inform management practices that balance sustainable waste management and safe food animal production, supporting farmers with improved knowledge and protection of animal health. Outreach efforts will include scientific publications, reports to farmers, and presentations at meetings involving stakeholders in the poultry and composting industries.

    Project objectives from proposal:

    1) Develop a novel screening method to determine the prevalence of ARGs in unprocessed food waste received by selected poultry farms in Vermont. Utilizing core facilities at the University of Vermont and extensive literature review, we will establish a protocol for shotgun metagenomic sequencing of food waste samples. We will obtain samples from 3 poultry farms accepting food waste/scraps in Vermont and analyze these samples using our shotgun metagenomic pipeline developed for this project. Four sample types will be collected per farm in order to fully assess ARGs belonging to food wastes and their persistence throughout the system, including food wastes, raw manures, on-farm finished composts, and eggs. Samples will be taken at 2 time points (shipments) and 10 samples per time point for each of the 4 sample types (to be composited), for a total of 8 composite samples per farm. Food wastes are known to contain antimicrobial resistant microorganisms, but little is known about the breadth of mobile genetic elements, including antimicrobial resistance genes (ARGs), which may also be carried. Data from this objective will be used to assess the risk of bringing these materials onto farms and will inform the management and handling of these substances. Currently, food wastes can be directly fed to poultry so these results will be the first report of ARGs in food waste informing producers, regulators and consumers if additional processing is necessary.

    Specific aims include:

    a) Identify target genes of interest for screening and create a comprehensive reference database for sequencing,

    b) Identify target genes with known primers for validation of metagenomic analysis,

    c) Identify antimicrobial resistance genes (ARGs) in food waste samples taken from poultry farms, and

    d) Categorize the types and abundance of ARGs identified in food waste samples obtained from poultry farms.


    2) Quantify the diversity of food waste management practices being implemented on integrated composting and poultry farms in Vermont. In the face of growing antimicrobial resistance concerns, characterizing farmers’ current awareness and efforts to prevent ARG introduction and spread is critical. For the 3 study farms, we will complete a survey to assess the level of knowledge about proper food waste handling and identify measures already being taken to prevent the spread or growth of antimicrobial resistance.

    Specific aims include:

    a) Assess the level of knowledge of poultry farmers about limiting antimicrobial resistance and

    b) Identify measures utilized at the farm level to reduce antimicrobial resistance.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.