Poultry litter harbors agents that generate antibiotic multi-resistance

Scientists may need to reexamine assumptions about the spread of antibiotic-resistant genes, according to a new study by researchers at the University of Georgia. They found that poultry litter – a ubiquitous part of large broiler operations – harbors a vastly larger number of microbial agents that collect and express resistance genes than was previously known.

The study, published today in the Proceedings of the National Academy of Sciences, shows that waste left behind by flocks raised in industrial chicken houses is rich in genes called integrons that promote the spread and persistence of clusters of varied antibiotic resistance genes.

“We were surprised to find a vastly greater pool of these multi-resistance clustering agents than anyone had suspected before,” said Anne Summers, a microbiologist from UGA who led the study. “Finding such a huge reservoir of integrons explains a long-standing puzzle about how clusters of resistance genes spread so rapidly and persist in bacterial communities even after antibiotic use concludes.”

Other authors of the paper included Sobhan Nandi, a postdoctoral associate in the UGA department of microbiology; and John Maurer and Charles Hofacre of the department of avian medicine in UGA’s College of Veterinary Medicine. Maurer also holds an appointment with the Center for Food Safety in Griffin.

Antibiotic resistance is a serious and growing problem for farm animal operations and human health. Antibiotic use in treating disease and increasing feed efficiency has been a common part of industrial farms for more than half a century. When antibiotic-resistant bacteria began to show up in hospitals in the 1950s, researchers initially believed that simply restricting the use of antibiotics on farms could reduce the prevalence of antibiotic resistance among humans, but it hasn’t been that easy.

“Over the past 30 years, we have learned this hope was unrealistic because we share both pathogenic and benign bacteria with other humans and animals,” said Summers, “and because bacteria transfer genes among themselves.”

At the heart of the multi-resistance problem are integrons, which scientists until now have exclusively studied in such pathogenic bacteria as Salmonella and E. coli. The UGA team wondered, however: Does the poultry production environment also harbor integrons that assemble these large clusters of distinct resistance genes?

To find out, they collected samples of poultry litter from Georgia broiler houses regularly over a 13-week period. Litter begins as a bedding material of softwood shavings placed in commercial broiler houses before chicks are brought to it. By the time the flock is harvested, the shavings have become mixed with chicken feces, uric acid, skin, feathers, insects and small invertebrates. Rich in minerals, poultry litter is often recycled for fertilizer, among other uses.

What the researchers discovered was startling: One integron type, called intl1 (typically found in E. coli and Salmonella) was up to 500 times more abundant than these bacteria themselves were in litter. A bit of microbial sleuthing revealed that integrons are also carried by so-called Gram positive bacteria that are much more abundant in litter than the E. coli-type bugs, called Gram negative bacteria.

“The fact that integron genes in the Gram positive bacteria are identical to those of E. coli indicates they are being actively exchanged among these otherwise unrelated bacteria,” said Summers. “Just as intriguing, integrons and resistance genes were abundant regardless of antibiotic use on the farms, suggesting that, once acquired, integrons are inherently stable, even without continual exposure to antibiotics.”

The study has several significant implications said Summers. Most studies of antibiotic resistance have been done in hospital settings, and until recently, much less work has been done on the real-world ecology of these systems that create multiply-resistant clusters. Knowledge about how antibiotic resistances spread from animals to humans is at present sketchy; however, since humans and their pets are “colonized” by similar bacteria, it is reasonable to think we and our companion animals also harbor such multi-resistance gene clusters that are enriched when we take an antibiotic ourselves or treat our pets.

Humans and animals have billions of bacteria in and on their bodies at any time, and even if resistance to a single antibiotic arises in a few of them through mutation, there are still several other antibiotics that can eliminate them. But if bacteria in the same environment are already equipped with clusters of genes conferring resistance to many antibiotics and can readily exchange these clusters, then the treatment options are limited.

“That’s what we have today, and the surprising abundance of integrons in the environment is a key as to why we have this problem,” said Summers.

The discovery is now leading Summers and her colleagues in microbiology and the College of Veterinary Medicine at UGA to see whether these resistance-gene-clustering systems are present in previously unrecognized reservoirs in companion animals and humans. The results will change our understanding of where resistance to new antibiotics will develop and how fast and how far it will spread and have implications for all antibiotic use, not just that in agriculture.

The research was supported by a grant from the National Research Initiative of the U.S. Department of Agriculture and made possible by four anonymous poultry producing companies that afforded free access to their facilities for sample collection.