Occurrence and reservoirs of antibiotic resistance genes in the environment

Antibiotic resistance genes have become highly mobile since the development of antibiotic chemotherapy. A considerable body of evidence exists proving the link between antibiotic use and the significant increase in drug-resistant human bacterial pathogens. The application of molecular detection and tracking techniques in microbial ecological studies has allowed the reservoirs of antibiotic resistance genes to be investigated. It is clear that the transfer of resistance genes has occurred on a global scale and in all natural environments. The considerable diversity of bacteria and mobile elements in soils has meant that the spread of resistance genes has occurred by all currently known mechanisms for bacterial gene transfer. Trans-kingdom transfers from plants to bacteria may occur in soil. Hot spots for gene transfer in the soil/plant environment have been described and colonized niches such as the rhizosphere and other nutrient-enriched sites, for example manured soil, have been identified as reservoirs of resistance genes. Although exposure and selection for tolerance of antibiotics is considerable in clinical environments there is increasing evidence that selection for resistant phenotypes is occurring in natural environments. Antibiotic-producing bacteria are abundant in soil and there is evidence that they are actively producing antibiotics in nutrient-enriched environments in soil. In addition there is clear evidence that the self-resistance genes found within antibiotic gene clusters of the producers have transferred to other non-producing bacteria. Perhaps most important of all is the use of antibiotics in agriculture as growth promotants and for treatment of disease in intensively reared farm animals. These treatments have resulted in gut commensal and pathogenic bacteria acquiring resistance genes under selection and then, due to the way in which farm slurries are disposed of, the spread of these genes to the soil bacterial community. Integrons with multiple resistance gene cassettes have been selected and disseminated in this way; many of these cassettes carry other genes such as those conferring heavy metal and disinfectant resistance which have been co-selected in bacteria surviving in effluents and contaminated soils, further maintaining and spreading the antibiotic resistance genes.