Comparing the effects of different manure treatment strategies on the presence of antimicrobial pollutants in treated manure on Pennsylvania dairy farms

The livestock industry is a major consumer of antibiotics and as such is a contributor to antimicrobial resistance (AMR). Livestock manure is a large repository of antimicrobial resistant genes (ARGs) and requires treatment before its application to agricultural land. Treatment of manure by composting or anaerobic digestion (AD) may reduce the prevalence of ARGs in manure, but few studies have comprehensively examined the fate of AMR pollutants in treated manure. In this pilot study, treated and untreated manure samples were collected from four dairy farms in Southeastern Pennsylvania. Two of these farms employed an anaerobic digester for manure treatment, one farm used a traditional composting method, and one farm heated their manure in a process that simulated the heating aspect of composting. The samples were extracted for genomic DNA, pooled, and subjected to metagenomic sequencing. The percentage of ARGs in treated samples from both AD farms was higher in treated than in corresponding untreated samples, while the opposite was true for traditional and modified composting farms. At the resistome level, all four untreated samples were similar, while there was considerable variability in the four treated samples. Untreated samples were dominated by ARGs conferring resistance to elfamycin and rifampin, and the prevalence of these ARGs in treated samples varied. Interestingly, ARGs conferring resistance to aminoglycosides were higher in treated samples than untreated samples from all four farms. This study demonstrates that both AD and composting affect the resistomes of manure, but these effects are variable; further studies are needed to better understand the conditions needed to effectively remove AMR pollutants.