Hyperthermophilic composting of livestock waste drastically reduces antimicrobial resistance

Composting is the most common method for managing livestock waste. However, it often fails to effectively eliminate antimicrobial resistance, resulting in potential antimicrobial resistance in livestock waste. Hence, a more effective livestock waste management strategy is warranted. The hyperthermophilic composting method uses recycled compost containing hyperthermophilic microbes to raise the compost temperature up to approximately 100 °C (compost temperature in normal composting: 50–70 °C). This study clarifies the effectiveness of hyperthermophilic composting method in attenuating antimicrobial resistance during livestock waste composting in both a composting simulator and on a field dairy farm. We analyzed bacterial abundance and community composition, performed PCR analysis, and evaluated the concentration of residual antimicrobials in the compost. Hyperthermophilic composting significantly reduced the abundance of culturable bacteria and Escherichia coli including that of antimicrobial-resistant culturable bacteria and E. coli in both the simulated and field dairy farms. The copy numbers of the tested antimicrobial resistance genes (tetA, tetB, bla_TEM, and bla_CTX-M) decreased substantially. Residual antimicrobials (tetracyclines and β-lactams) were not detected in the field dairy farms, and network analysis showed that potential hosts of antimicrobial-resistance genes were eliminated. These results indicate that hyperthermophilic composting significantly reduces the abundance of antimicrobial-resistant bacteria, antimicrobial-resistance genes, and residual antimicrobials at low cost and easy operation while generating valuable agricultural resource as the final output.