Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities

Authors: Burch, Tucker; FIRNSTAHL, AARON - U.S. GEOLOGICAL SURVEY (USGS); SPENCER, SUSAN; LARSON, REBECCA - UNIVERSITY OF WISCONSIN; BORCHARDT, MARK

Submitted to: Journal of Environmental Quality
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2022
Publication Date: 4/28/2022
Citation: Burch, T.R., Firnstahl, A.D., Spencer, S.K., Larson, R.A., Borchardt, M.A. 2022. Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities. Journal of Environmental Quality. 51(3):352-363. https://doi.org/10.1002/jeq2.20350.
DOI: https://doi.org/10.1002/jeq2.20350

Interpretive Summary: Antimicrobial resistance (AMR) is a global public health problem, contributing to 2.8 million infections in the United States annually. AMR is mediated by antibiotic resistance genes (ARGs), which are increasingly regarded as environmental pollutants. Livestock manure is a major environmental reservoir of ARGs, and anaerobic digestion of livestock manure has been suggested as an intervention to limit the spread of ARGs to the environment. However, most studies on the fate of ARGs during anaerobic digestion of livestock manure have been conducted in laboratory settings, and very few have examined their fate in full-scale digesters on commercial livestock production facilities. This study sampled untreated manure and treated digestate from 7 full-scale digesters treating dairy manure over the course of 3 different seasons and examined the relative effects of digestion, season, and facility. Results indicate that real-world performance of anaerobic digestion for removal of ARGs is less than expected compared to previous laboratory-based studies. This suggests a need for a multiple barrier approach when it comes to controlling discharge of ARGs from livestock production facilities. Results also illustrate that seasonal and facility-to-facility variation in ARG concentrations are quantitatively comparable to the digestion effect itself. This emphasizes the need to more fully investigate sources of variation in ARG concentrations across seasons and facilities in order to elucidate further management controls on the proliferation of antimicrobial resistance.

Technical Abstract: Anaerobic digestion has been suggested as an intervention for the spread of antibiotic resistance genes (ARGs) from livestock manure and typically been investigated at laboratory scale. Few studies have quantified ARG fate during full-scale digestion of livestock manure. This study sampled untreated manure and treated digestate from 7 full-scale digesters treating dairy manure. Samples were collected biweekly from December through August (i.e., during Winter, Spring, and Summer; n = 235 total) and analyzed by quantitative polymerase chain reaction for intI1 and the ARGs ermB, sul1, tetA, and tetW. Concentrations of intI1, sul1, and tetA declined during anaerobic digestion, but their log removal was lower than expected based on previous laboratory studies. Log removal for intI1 during anaerobic digestion equaled 0.28 ± 0.03 log10 units (mean ± standard error), which was notably low and important given intI1’s role in horizontal gene transfer and multiple resistance. Furthermore, tetW concentrations were unchanged during anaerobic digestion (p > 0.05), and ermB concentrations increased by 0.52 ± 0.03 log10 units (i.e., 3.3-fold), which is important given erythromycin’s status as a critically important antibiotic for human medicine. Finally, seasonal log10 changes in intI1, sul1, and tetA concentrations were = 50% of corresponding log removals by anaerobic digestion, and variation in ARG and intI1 concentrations among digesters was quantitatively comparable to anaerobic digestion effects. Overall, these results suggest that anaerobic digestion may be limited as an intervention for ARGs in livestock manure and emphasize the need for multiple farm-level interventions to limit the spread of antibiotic resistance.