The emergence of multidrug-resistant pathogens has made antibiotic resistance one of the most significant global health threats of our time. Antibiotic resistance has been recently linked to anthropogenic reservoirs such as animal husbandry facilities; and although this phenomenon is traditionally associated with the use of antibiotics as prophylactics/growth promoters, it may also be linked to additional factors. We hypothesize that animal feed may be a driver of antibiotic resistance in the feed-gut-feces continuum, and therefore determined the magnitude and scope of antibiotic resistance in microbiomes of wheat and corn/sorghum silage from commercial cattle feeding centers. Analysis of silage bacterial community composition in feedstocks revealed that the center of the silage bunkers (pH ~3.8) was almost completely dominated by Lactobacillus (>90%); whereas in the air-exposed shoulders of the bunker (pH ~6.8), Lactobacillus abundance was below 5% and Enterobacteriaceae became a significant fraction of the community. We isolated large libraries of silage-derived Lactobacillus and Enterobacteriaceae strains and screened them on ampicillin, tetracycline, ciprofloxacin, ceftriaxone, erythromycin kanamycin and vancomycin. Surprisingly, the vast majority of lactobacilli isolates (1868/188) were resistant to all the seven tested antibiotics, whereas the Enterobacteriaceae isolates were resistant to 2-5 of the five antibiotics. Interestingly, the presence of 3 prominent clinically-associated extended-spectrum β–lactamases were detected in both Enterobacteriaceae and Lactobacillus isolates suggesting that these genes may be horizontally transferred in the course of silage fermentation. This study demonstrates the vast scope of antibiotic resistance in silage, which may contribute to antibiotic resistance propagation along the food chain.
