Metagenomic-Based Evidence of Antimicrobial Resistance Gene Distributions on Dairy Farms.

Antimicrobial resistance (AR) is a global phenomenon with serious health implications.  In modern animal production systems, antimicrobials are commonly used for therapeutic and/or non-therapeutic purposes.  This has led to the development of AR genes in animals and the subsequent shedding of these resistant agents in feces.  However, information is lacking regarding the distribution pattern and dissemination of AR genes across the farming sectors.   Using next generation sequencing technology, we investigated the spatial distribution of AR genes on dairy farms from animal quarters to the field.  Samples of cow feces (freshly produced), manure (from storage facilites), and field soil (where manure is applied) were obtained from five dairy farms in Northeast USA and extracted for genomic DNA.  Metagenomic libraries were constructed and screened for phylogeny (microbiome) and AR genes (resistome).  The microbiomes of feces, manure and soil samples had distinct phylogenetic compositions (P<0.001) irrespective of farms. This indicates that the microbial makeup of the relevant farm sectors is resilient to potential microbial perturbation.   In contrast, the resistome of the samples exhibited certain similarities.  A group of AR genes (ARa, bcra, macb, mdtf, pbp1a, tetl, tetm, teto, tetq, tets, tetw, vanra, and vanrbAR genes) were present in all samples of all farms and constituted the dominating AR genes.  This group of AR genes confer resistance to multiple antibiotics, including macrolides, amphenicols, and tetracyclines.   In addition, fecal and manure resistomes contained AR genes specific for quinolones, sulfonamides, aminoglycosides and beta-lactams.  The abundance of AR genes varied with sample type (P<0.05); farms differed considerably in terms of the abundance, diversity, and distribution of AR genes.  Nevertheless, all farms showed that manure was the hot spot with AR gene abundance and diversity greater than feces and soils.   For the first time, we provide metagenomic-based evidence that AR genes are widespread across the major farming sectors and that manure may function as the main vehicle for AR gene dissemination, subsequently contaminating food and waters.

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