Abstract
There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.
Highlights
American consumers and producers are increasingly aware of concerns over antibiotic resistance in food
The specific concern is that the use of antibiotics in food animals promotes the growth of antibiotic resistant bacteria that can be transferred to humans via food processing and distribution systems [1]
Even if the bacteria themselves do not survive outside of the live animal, their antibiotic resistance genes may be available for uptake by other bacteria via a process called horizontal gene transfer (HGT)
Summary
American consumers and producers are increasingly aware of concerns over antibiotic resistance in food. The specific concern is that the use of antibiotics in food animals promotes the growth of antibiotic resistant bacteria that can be transferred to humans via food processing and distribution systems [1]. If these antibiotic resistant bacteria survive the acid pH of the stomach, they can potentially infect humans and cause disease. We identified bacteria that are likely carrying the antibiotic resistance genes, and determined if there are differences in the diversity or taxonomic distribution of antibiotic resistant bacteria in agricultural and natural settings
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