Composting Swine Slurry to Reduce Indicators and Antibiotic Resistance Genes


Over the last twenty years there have been considerable increases in the incidence of human infections with bacteria that are resistant to commonly used antibiotics. This has precipitated concerns about the use of antibiotics in livestock production. Composting of swine manure has several advantages, liquid slurries are converted to solid, the total volume of material is reduced and the stabilized product is more easily transported off-site. The goal of this study was to determine if composting can also be used to reduce the concentration of indicators and bacteria containing genes for antibiotic resistance (AR) in swine manure.

What did we do? 

Sample Analysis:

Compost trials were conducted in either fall (FT) or spring (ST) and piles were turned once, three times or upon reaching 65 ºC. Microbial indicators and populations with AR genes for tetracycline, erythromycin and sulfonamide resistance were quantified by culture and/or quantitative, real-time (qPCR) analysis.

Compost materials and conditions:

Decomposed materials (a mixture of swine slurry and woodchips) were obtained on two separate occasions from swine high-rise finishing facilities (HRFF) located in western Kentucky. The HRFF houses between 4,000 and 4,800 swine which are placed in the facility at 18 to 20 kg and are removed after three months (weighing about 105 kg). The high-rise floor raises the living area 3.7 m above the ground. Manure, excess feed, water and wastewater drop through slatted floors into 2.5 cm screened woodchips (average size 1.9 ± 0.9 cm). The slurry-woodchip material was turned up to three times per week while under the HRFF. When the material was visibly moist, reducing its ability to absorb additional waste materials, it was removed from the facility for finishing in windrows. In fall 2011 (FT) and Spring 2012 (ST), HRFF slurry-woodchip mix (approximately 60 m3 weighing 48.4 Mg) was brought by semi-trailer trucks to the Western Kentucky University Agricultural complex where ma terials were divided into three or four windrow piles. In the FT, swine slurry-woodchip mixes having a bulk density of 849.6 kg m-3 and consisting of around 19.6 m3 of material were formed into three piles of approximately 10.4 m x 2.1 m x 0.9 m (L x W x H). In the ST, swine slurry-woodchip mixes having a bulk density of 778.4 kg m-3 and consisting of around 18.8 m3 of material were formed into three piles of approximately 5.8 m x 2.7 m x 1.2 m (L x W x H) and a fourth batch (unturned) was left piled at the side (0X; 3.6 m3). In each study, piles were turned using a windrow compost turner either once per week (1X), three times per week (3X) or upon the internal compost temperature reaching 65 ºC (@65). Compost for the FT @65 treatment heated to 65 ºC by day 14 and was turned 11 times over the course of the trial. However, during the ST, the @65 pile did not heat for the first 63 days (mean temperature 27 ± 8 ºC) therefore weekly turning was initiated at that time. Samples were taken on days 0 and three and then weekly for the first 12 weeks and bi-weekly until composting was stopped at day 112 for the FT and day 142 for the ST.

What have we learned? 

In the FT, concentrations of enterococci decreased below culturable detection within 21 days, corresponding with a 99% decrease in detection by qPCR (Fig. 1). Similar decreases in qPCR detection in the ST took longer (day 49 or day 77 of composting). Changes in the concentration of bacteria with AR genes varied by antibiotic type (erythromycin (36% – 97%), tetracycline (94% to 99%) and sulfonamide (53% to 84%) and compost season (greater decreases in ST). There were few differences based on turning regime. Even the unturned compost pile had 90%, 98% and 56% reduction in bacteria resistant to erythromycin, tetracycline and sulfonamide, respectively.

Results suggest that composting effectively decreases the concentration of indicators and AR genes in swine manure. As concerns over antibiotic resistance and pathogens increase, composting provides a valuable manure management tool for decreasing contaminants and improving the value of this material as a soil conditioner.

Future Plans    

Volume reduction, low moisture and low readily degradable organic matter suggest that the finished compost would have lower transportation costs and should provide value as a soil conditioner. Studies are warranted to evaluate its agronomic value as an alternative source of plant nutrients. Future studies will be conducted to evaluate the nutrient value this compost as an organic fertilizer for row crop production.


Kimberly Cook, Research Microbiologist, USDA ARS

Carl Bolster, USDA ARS; Karamat Sistani, USDA ARS

Additional information        


This research was conducted as part of USDA-ARS National Program 214: Agricultural and Industrial By-products: CRIS 6445-12630-004-00D. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

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