Antibiotic resistance genes in human pathogens such as methicillin-resistant Staphylococcus aureus 1 have become notorious because they confound the tools that are used to treat disease (FIG. 1). In particular, resistance determinants in pathogens are commonly encountered after the introduction of an antibiotic to clinical use, and treating human pathogens with anti- biotics directly affects the frequency of resistance to those antibiotics in these pathogens 1–4 . The presence of antibiotic resistance elements in pathogenic bacteria is made all the more problematic because of the prevalence of horizontal gene transfer, the process by which bacteria acquire genes from the environment 5 . Many of the known antibiotic resist- ance genes are found on transposons, integrons or plasmids, which can be mobilized and transferred to other bacteria of the same or different species. There is evidence of the transfer of resistance elements to known human commensal bacteria and pathogens 6,7 , and gene transfer in the human intestinal microbiome is extensive 8 . What are the sources and reservoirs of these transferable genes? A full understanding of the pres- sures and circumstances that lead to the evolution and dissemination of antibiotic resistance genes in pathogens is impossible without a detailed examina- tion of the origin and role of resistance genes in natural environments. This Review discusses the environmen- tal sources of antibiotic resistance, the functions and roles of resistance genes in microbial ecology and the ways by which those genes may be disseminated in response to human antibiotic use. Selection pressures in the environment Antibiotics are essential for the treatment of bacterial infections in humans and animals; it is therefore a top priority to preserve their efficacy. For decades, clini- cians and scientists have called for the prudent use of antibiotics, in an effort to slow the development and epidemic spread of resistance 9–11 . Prudent use of anti- biotics in humans demands that physicians establish that a bacterial infection is responsible for the patient’s symptoms before an antibiotic prescription is written. By contrast, in agriculture antibiotics are used in the absence of acute infection. Some of the same antibiot- ics that are used to treat human pathogens, such as amoxicillin and erythromycin, are also used to treat disease, promote growth and improve feed efficiency in animals 12 ( BOX 1). Just as in hospital settings, the agricultural use of antibiotics selects for antibiotic resistance, arguably in a more widely disseminated fashion owing to the farm-wide administration of prophylactic antibiotics in feed and water. Antibiotics from both urban and agricultural sources persist in soil and aquatic environments, and the selective pres- sure imposed by these compounds may affect the treat- ment of human diseases 13,14 . As another example, the prophylactic use of antibiotics in fish farms has led to a rise in the number of resistant bacteria 15 . Strikingly, these resistant bacteria can transfer the resistance genes to human pathogens 16 . The selection pressure applied by the antibiotics that are used in clinical and agricultural settings has promoted the evolution and spread of genes that confer resistance, regardless of their origins (FIG. 2). * Departments of Bacteriology and Plant Pathology, University of Wisconsin– Madison. ‡ Microbiology Doctoral Training Program, University of Wisconsin–Madison, 1550 Linden Dr., Madison, Wisconsin 53706, USA. § Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T1Z3, Canada. || Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA. Correspondence to J.H. e-mail: jo.handelsman@yale.edu doi:10.1038/nrmicro2312 Published online 1 March 2010 Call of the wild: antibiotic resistance genes in natural environments Heather K. Allen *‡ , Justin Donato * , Helena Huimi Wang § , Karen A. Cloud-Hansen * , Julian Davies § and Jo Handelsman || Abstract | Antibiotic-resistant pathogens are profoundly important to human health, but the environmental reservoirs of resistance determinants are poorly understood. The origins of antibiotic resistance in the environment is relevant to human health because of the increasing importance of zoonotic diseases as well as the need for predicting emerging resistant pathogens. This Review explores the presence and spread of antibiotic resistance in non-agricultural, non-clinical environments and demonstrates the need for more intensive investigation on this subject. REVIEWS NATURE REVIEWS | MICROBIOLOGY ADVANCE ONLINE PUBLICATION | 1 Nature Reviews Microbiology | AOP, published online 1 March 2010; doi:10.1038/nrmicro2312 FOCUS ON ANTIMICROBIAL RESISTANCE © 20 Macmillan Publishers Limited. All rights reserved 10