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Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. In this study piglets were birthed at the National Animal Disease Center in Ames, IA, and housed together in highly-controlled, decontaminated rooms to avoid cross contamination among the medicated animals, nonmedicated animals, and other resident barn animals. Neither the piglets nor the sow were exposed to antibiotics before the study. This design was to ensure that the inoculum for the piglets would come horizontally from their mother, minimizing variability so that effects of antibiotic treatment could be detected. At 18 wk of age, one group of littermates received diet containing performance-enhancing antibiotics (chlortetracycline, sulfamethazine, and penicillin) and the other portion receiving the same diet but without the antibiotics for 3 wk. Fecal samples were collected just before treatment (day 0), and after 3, 14, and 21 d of continued treatment. Day 0 samples were used to describe the swine intestinal microbiome before antibiotic treatment period. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1–11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations.
Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.
Torey Loofta, et al. In-feed antibiotic effects on the swine intestinal microbiome. PNAS January 17, 2012.