Effectiveness of Different Dairy Manure Management Practices in Controlling the Spread of Antibiotics and Antibiotic Resistance

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Even when antibiotics are used judiciously, antibiotic residues, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) can accumulate in human waste and manure and contribute to the spread of antibiotic resistance. Modern U.S. dairy farms use antibiotics for disease treatment and prevention according to the guidance of veterinary physicians. While dairy manure handling and treatment systems may effectively mitigate antibiotic resistance, the fate of antibiotic residues, ARB and ARG through these systems has not been adequately investigated. 

What did we do? 

Working cooperatively with 11 dairies in 3 states (NY, PA, MD) our multi-institutional (U. Buffalo, Cornell, U. Maryland, U. Michigan), interdisciplinary team is investigating the effect different manure management practices (e.g. long-term storage, composting, anaerobic digestion, etc.) have on antibiotic residue levels, ARB and ARG. Every 6 weeks for 2 years manure is being collected pre- and post- each treatment step of the various manure handling systems used by each farm. All samples are being characterized and tested for select antibiotic residues (tetracyclines, macrolides, sulfonamides, penicillins and ceftiofurs), with select samples also analyzed for ARB and ARG. To guide these efforts, antibiotic usage and manure treatment system operational data are also being collected for each farm.

What have we learned? 

A year of samples has been collected with analysis of antibiotic residues, ARB and ARG on-going. Based on the preliminary data, antibiotic residues are detectable at low-concentrations (< 200 mg/L) in each farm’s manure. Antibiotic residue levels are generally lower in treated manure compared to levels in raw manure, though mitigation efficacy is variable. Early findings show some composting systems have the capacity to lower antibiotic residue levels. Antibiotic residue levels are also lower in separated manure solids, with evidence for partitioning of soluble antibiotic residues into separated manure liquids. At this time, the effects of anaerobic digestion and long-term anaerobic manure storage on antibiotic residue levels remain unclear. Select samples are currently being analyzed for ARB and ARG.

Future Plans 

We are entering our second year of field monitoring and ARB and ARG analysis is on-going. Laboratory efforts are also beginning to test the effectiveness of specific anaerobic digester operational parameters at mitigating antimicrobial resistance. Extension/outreach meetings with stakeholder groups are also being planned. The ultimately project goals are to discern the fate of antibiotic residues, ARB and ARG as they move through dairy manure handling systems, identify the efficacy of different manure treatment systems at mitigating antibiotic resistance and extending this knowledge to dairy operators.

Corresponding author, title, and affiliation      

Jason Oliver, Postdoctoral Associate at Dept. of Animal Science, Cornell University

Corresponding author email    


Other authors   

Curt Gooch, Senior Extension Associate at Cornell University, Dept. of Animal Science, PRO-DAIRY

Additional information               

Additional project information can be found on the dairy environmental system webpage: www.manuremanagement.cornell.edu


This material is based upon work that is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award number 2016-68003-24601. 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.

Project collaborators include: (PD) Diana Aga, University of Buffalo, Dept. of Chemistry (Co-PI); her students Mitch Mayville and Jarod Hurst; (Co-PD) Lauren Sassoubre , University of Buffalo, Dept. of Civil, Structural & Environmental Engineering; (Co-PDs) Stephanie Lansing and Gary Felton, Associate Professors at University of Maryland, Dept. of Environmental Science & Technology; their student Jenna Schueler; (Co-PD) Krista Wigginton, Assistant Professor at University of Michigan, Dept. of Civil & Environmental Engineering; Lutgarde Raskin, Professor at University of Michigan, Dept. of Civil & Environmental Engineering; and their student Emily Crossette.


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