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

Antibiotic resistance genes (ARGs) are emerging environmental contaminants of concern to both human and animal health. Dairy manure is considered reservoir of ARGs. This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common manure management. A total of 33 manure samples were collected from multiple manure treatment conditions: 1) flushed manure (FM), 2) fresh pile (FP), 3) compost pile (CP), 4) primary lagoon (PL), and 5) secondary lagoon (SL). After DNA extraction, all fecal samples were screened by PCR for the presence of 8 ARGs: four sulfonamide ARGs (sulI, sulII, sulIII, sulA), two tetracycline ARGs (tetW, tetO), two macrolide-lincosamide-streptogramin B (MLSB) ARGs (ermB, ermF). Samples were also screened for two mobile genetic elements (MGEs) (intI1, tnpA), which are responsible for dissemination of ARGs. Quantitative PCR was then used to screen all samples for five ARGs (sulII, tetW, ermF, tnpA and intI1). Prevalence of genes varied among sample types, but all genes were detectable in different manure types. Results showed that liquid-solid separation, piling, and lagoon conditions had limited effects on reducing ARGs and MGEs, and the effect was only found significant on tetW (p = 0.01). Besides, network analysis indicated that sulII was associated with tnpA (p < 0.05), and Psychrobacter and Pseudomonas as opportunistic human pathogens, were potential ARG/MGE hosts (p < 0.05). This research indicated current manure management practices in California dairy farms has limited effects on reducing ARGs and MGEs. Improvement of manure management in dairy farms is thus important to mitigate dissemination of ARGs into the environment.