Chicken coops push antibiotic resistance

The research, led by a team at Washington University School of Medicine in St. Louis, is published in Nature. From chicken coops and composting latrines to sewage treatment plants and city parks, a new study conducted in El Salvador and Peru identifies places where people are likely to encounter bacteria that can transmit antibiotic resistance.

The scientists surveyed bacteria and their capacity to resist antibiotics in a rural village in El Salvador and a densely populated slum on the outskirts of Lima, Peru. In both communities, the researchers identified areas ripe for bacteria to shuffle and share their resistance genes. These hot spots of potential resistance transmission included chicken coops in the rural village and a modern wastewater treatment plant outside Lima.

“Bacteria can do this weird thing that we can’t: exchange DNA directly between unrelated organisms,” said senior author Gautam Dantas, PhD, an associate professor of pathology and immunology. “That means it’s relatively easy for disease-causing bacteria that are treatable with antibiotics to become resistant to those antibiotics quickly. If these bacteria happen to come into contact with other microbes that carry resistance genes, those genes can pop over in one step. We estimate that such gene-transfer events are generally rare, but they are more likely to occur in these hot spots we identified.”

While the study was done in developing parts of the world, Dantas suggested ways the data could be relevant for the U.S. and other industrialized countries. If the chicken coops of subsistence farmers are hot spots of resistance gene transfer, he speculated that bacteria present in industrial farming operations – where chickens regularly receive antibiotics – would see even more pressure to share resistance genes. Dantas expressed concern about such bacteria getting into the food system. Further, the wastewater treatment facility the investigators studied in Lima is a modern design that uses technologies typical of such facilities around the world, including those in the U.S., suggesting these plants may be hot spots of antibiotic resistance transmission regardless of their locations.

The study is the first to survey the landscape of bacteria and the genetics of their resistance across multiple aspects of an environment, including the people, their animals, the water supply, the surrounding soil, and samples from the sanitation facilities. While the densely populated slum surrounding Lima has a districtwide sewage system and modern wastewater treatment plant, the village in El Salvador has composting latrines.

Rural villagers who rely on subsistence farming, and residents of densely populated, low-income communities surrounding cities make up a majority of the global population; yet their microbiomes are largely unstudied. Most similar studies to date have focused on heavily industrialized populations in the United States and Europe and on rare and so-called pristine communities of people living a traditional hunter-gatherer lifestyle.

“Not only do the communities in our study serve as models for how most people live, they also represent areas of highest antibiotic use,” Dantas said. “Access to these drugs is over-the-counter in many low-income countries. Since no prescription is required, we expect antibiotic use in these areas to be high, putting similarly high pressure on bacteria to develop resistance to these drugs.”

In general, Dantas and his colleagues found that resistance genes are similar among bacteria living in similar environments, with more genetic similarity seen between bacteria in the human gut and animal guts than between the human gut and the soil, for example. In addition, the researchers also found that bacteria that are closely related to one another have similar resistance genes, which might be expected as bacteria pass their genes from one generation to the next.