Distribution and Quantification of Antibiotic Resistant Genes and Bacteria across Agricultural and NonAgricultural Metagenomes

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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

 

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