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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #391408

Research Project: Sustainable Management of Manure Nutrients and Environmental Contaminants from Beef and Swine Production Facilities

Location: Livestock Bio-Systems

Title: Composting reduces the risks of resistome in beef cattle manure at the transcriptional level

Author
item SUN, YUEPENG - University Of Nebraska
item STALEY, ZACHERY - University Of Nebraska
item Woodbury, Bryan
item RIETHOVEN, JEAN-JACK - University Of Nebraska
item LI, XU - University Of Nebraska

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2024
Publication Date: 3/6/2024
Citation: Sun, Y., Staley, Z.R., Woodbury, B., Riethoven, J., Li, X. 2024. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level . Applied and Environmental Microbiology. 90. Iss 4. https://doi.org/10.1128/aem.01752-23.
DOI: https://doi.org/10.1128/aem.01752-23

Interpretive Summary: Composting and stockpiling are two common practices for managing manure prior to land application. It is thought that composting would do a better job controlling the genes associated with antibiotic resistance when compared to stockpiling. This study was designed to determine which storage method (composting or stockpiling) was better for reducing the potential of spreading antibiotic resistance genes in the environment through manure. The impact of location within the storage pile was also evaluated for reducing antibiotic resistance genes. Results indicate that composting was better than stockpiling in reducing the different types and amount of antibiotic resistance genes measured. Location within the storage pile had the greatest impact on reducing antibiotic resistant genes, with lower amounts of antibiotic resistance genes in the middle of both the stockpiled and composted manure storage. Although composting was better than stockpiling at reducing antibiotic resistance genes, further advances in managing composted manure are needed to further enhance this beneficial effect.

Technical Abstract: Transcriptomic evidence is needed to determine if composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.