Antibiotic-resistant infections make illnesses harder and more expensive to treat

The Department of Agriculture National Institute of Food and Agriculture awarded $294,000 to Cary Institute of Ecosystem Studies, Inc. on August 15, 2026, under the Agriculture and Food Research Initiative (AFRI, CFDA 10.310).

The recipient will conduct controlled greenhouse research measuring antibiotic-resistant bacteria and resistance genes in lettuce and carrots grown under four manure treatment conditions: no manure, raw manure, manure composted for 3 days, and manure composted for 15 days with regular re-mixing. Using DNA-based tools, the research team will track resistance presence from manure and compost through soil to harvested vegetables, determining whether resistance sits on vegetable surfaces (removable by washing) or inside plants (not removable). The work will establish whether composting practices reduce antibiotic resistance reaching raw produce and identify specific resistance genes involved.

Performance occurs at Millbrook, New York from August 15, 2026 through August 14, 2028. Cary Institute, a tax-exempt nonprofit ecosystem research organization, serves as the prime recipient.

Farms are one place resistance can spread. When livestock are treated with antibiotics, their manure can carry not only leftover drug residues but also the resistant bacteria themselves and the genes that make bacteria resistant. However, manure is also one of the most valuable ways american farmers return nutrients to the soil, improving soil health and reducing the need for chemical fertilizer. The concern is that when manure is spread on fields, these resistance genes can end up on and even inside the vegetables we eat, especially crops eaten raw. Composting, which heats manure to high temperatures before IT is applied, is widely assumed to solve this problem, yet the scientific evidence is genuinely mixed: some studies find composting reduces resistance, while others find IT stays the same or even increases. Farmers, regulators, and the public currently lack a clear, U.S.-based answer to a basic question, namely whether the composting practices we already recommend actually protect people from picking up antibiotic resistance through their food.to answer this, we will grow lettuce and carrots, two crops commonly eaten raw and representing both leafy and root vegetables, in a controlled greenhouse under four conditions: with no manure, with raw manure, with manure composted for a short time (3 days), and with manure composted for a longer time with regular RE-mixing (15 days). At each step, from the manure and compost through the soil to the harvested vegetables, we will use modern DNA-based tools to measure how much antibiotic resistance is present, whether IT sits on the surface of the vegetable (where washing might remove IT) or inside the plant (where IT cannot be washed off), and which bacteria are carrying IT. Our goal is to determine whether, and by how much, better composting reduces the resistance that reaches our food, and to pinpoint the specific resistance genes that pose the greatest risk. If successful, this project will give farmers evidence-based guidance for managing manure safely, help regulators set standards that address resistance genes and not just disease-causing germs, and lay the groundwork for larger farm-scale studies, ultimately helping protect the safety of the american food supply while preserving the soil-health benefits that manure provides.