Lagoon, Anaerobic Digestion, and Composting of Animal Manure Treatments Impact on Tetracycline Resistance Genes

Abstract

Increased demand for animal protein is met by increased food animal production resulting in large quantities of manure. Animal producers, therefore, need sustainable agricultural practices to protect environmental health. Large quantities of antimicrobials are used in commercial food animal production. Consequently, antimicrobial-resistant bacteria and the resistance genes emerge and are excreted through feces. Manure management is essential for the safe disposal of animal waste. Lagoons, with or without covers, and anaerobic digesters, with the primary purpose of methane production, and composting, with the primary purpose of producing organic fertilizer, are widely used methods of manure treatment. We reviewed manure management practices and their impact on tetracycline resistance genes. Lagoons are maintained at ambient temperatures; especially uncovered lagoons are the least effective in removing tetracycline resistance genes. However, some modifications can improve the performance of lagoons: sequential use of uncovered lagoons and the use of covered lagoons resulted in a one-log reduction, while post-treatments such as biofiltration following covered lagoon treatment resulted in 3.4 log reduction. Mesophilic digestion of animal manure did not have any significant effect; only a 0.7 log reduction in tet(A) was observed in one study. While thermophilic anaerobic digesters are effective, if properly operated, they are expensive for animal producers. Aerobic thermophilic composting is a promising technology if optimized with its economic benefits. Composting of raw animal manure can result in up to a 2.5 log reduction, and postdigestion composting can reduce tetracycline resistance gene concentration by >80%. In general, manure management was not designed to mitigate antimicrobial resistance; future research is needed to optimize the economic benefits of biogas or organic fertilizer on the one hand and for the mitigation of foodborne pathogens and antimicrobial resistance on the other.

Keywords: One Health; anaerobic digestion; animal manure; antimicrobial stewardship; composting; lagoons; tetracycline resistance genes.

Figure 1

Medically important antimicrobial drugs approved for use in food-producing animals actively marketed in the United States between 2010–2019. Others: Amphenicols, Diaminopyrimidines, Fluoroquinolones (excluding 2013 through 2019), Polymyxins (excluding 2012 and 2013), and Streptogramins. Data were analyzed from FDA 2020 [19]. Guidance for Industry #213 [17] states that all antimicrobial drugs and their associated classes listed in Appendix A of FDA’s Guidance for Industry #152 [18] are considered “medically important” in human medical therapy.

Figure 2

Anaerobic digestion systems registered in the United States for the treatment of animal manure. Frequency of anaerobic digestion facilities by (a) operation type; (b) year anaerobic digestion facility became operational; (c) animal production system (cattle refers to beef cattle); (d) State. Data were analyzed from the Agstar livestock AD database [62].

Figure 2

Anaerobic digestion systems registered in the United States for the treatment of animal manure. Frequency of anaerobic digestion facilities by (a) operation type; (b) year anaerobic digestion facility became operational; (c) animal production system (cattle refers to beef cattle); (d) State. Data were analyzed from the Agstar livestock AD database [62].