Addressing the Natural Antibiotic Resistome in Studies of Soil Resistance.

The environment is recognized as a source and a reservoir of antibiotic resistance (AR). Many antibiotic compounds are derived from bacteria and fungi that are naturally present in the environment. These microbes carry genes encoding resistance to the antibiotic that they produce and their resistance genes are often found in the same gene cluster as the antibiotic biosynthesis pathway though the actual rates at which this occurs in the natural environments or agroecosystems is unknown. Development of resistance in microbes is a natural evolutionary process that ensures survival and reproduction of species under stress in their preferred habitats.  The mechanisms driving the selection for AR are similar in human pathogens and in indigenous environmental bacteria; these adaptations could be influenced by exposure to (i) antibiotics; (ii) antibiotic resistant bacteria (ARB) including other non-pathogenic environmental organisms; and (iii) ARGs. With the knowledge that AR can originate from the microbiota present in terrestrial and aquatic agricultural ecosystems, protecting human health from excessive development of resistance in pathogens of clinical importance requires greater understanding of mechanisms responsible for selection of ARB in the environment.