Trends in Antimicrobial Resistance Genes in Manure Blend Pits and Long-Term Storage Across Dairy Farms with Comparisons to Antimicrobial Usage and Residual Concentrations

Abstract

The use of antimicrobials by the livestock industry can lead to the release of unmetabolized antimicrobials and antimicrobial resistance genes (ARG) into the environment. However, the relationship between antimicrobial use, residual antimicrobials, and ARG prevalence within manure is not well understood, specifically across temporal and locationbased scales. The current study determined ARG abundance in untreated manure blend pits and long-term storage systems from 11 conventional and one antimicrobial-free dairy farms in the Northeastern U.S. at six times over one-year. Thirteen ARGs corresponding to resistance mechanisms for tetracyclines, macrolides-lincosamides, sulfonamides, aminoglycosides, and β-lactams were quantified using a Custom qPCR Array or targeted qPCR. ARG abundance differed between locations, suggesting farm specific microbial resistomes. ARG abundance also varied temporally. Manure collected during the winter contained lower ARG abundances. Overall, normalized ARG concentrations did not correlate to average antimicrobial usage or tetracycline concentrations across farms and collection dates. Of the 13 ARGs analyzed, only four genes showed a higher abundance in samples from conventional farms and eight ARGs exhibited similar normalized concentrations in the conventional and antimicrobial-free farm samples. No clear trends were observed in ARG abundance between dairy manure obtained from blend pits and long-term storage collected during two drawdown periods (fall and spring), although higher ARG abundances were generally observed in spring compared to fall. This comprehensive study informs future studies needed to determine the contributions of ARGs from dairy manure to the environment.

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

“…Among soil samples, the sample from the small organic herd had a diverse pool of ARG including efflux pumps for multidrug resistance, MLS, rifampins, and tetracyclines. As per the history obtained from producers, the soils sampled during spring/summer received manure application about 6-9 months prior to sampling time thus indicating the influence of environmental factors on the distribution of diverse ARG in the soil sample; this is in agreement with the findings of Hurst et al [46] who reported that the abundance of ARG can be influenced by environmental factors such as location, antimicrobial use, farm type, antimicrobial concentrations, and storage of manure samples.…”

Metagenomic Quantification of Genes with Internal Standards

“…We used six manure samples from different farms and treatment stages (untreated, composted, or digested). Five target genes, tetM, tetG, sul1, sul2, and ermB, were chosen because they have frequently been quantified in environmental samples and primer sets are available (25)(26)(27)(28)(29). In the quantitative metagenomic approach, reads were assigned to ARGs in the Comprehensive Antimicrobial Resistance Database (CARD) using graphing resistance out of metagenomes or "GROOT" (Fig.…”

Quantification of antibiotic resistance genes and mobile genetic elements in manure from dairy farms in California

“…Authors found tet and sul ARGs in chicken layer lagoons were lowest compared with lagoons of swine and dairy facilities. Hurst et al (2019) studied the abundance of 13 ARGs in untreated manure blend pits and long-term storage systems in Northeastern U.S dairy farms, and a majority of farms use a scrape system to collect manure. The authors found ARGs abundance varied among farms, and ARG concentrations generally did not correlate to average antimicrobial usage due to complex environmental factors.…”