Scientists may need to re-examine 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 in the Proceedings of the National Academy of Sciences, reported that waste left behind by flocks raised in industrial chicken houses is rich in genes called integrons. Apparently they 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; as well as 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 restricting the use of antibiotics on farms could reduce the prevalence of antibiotic resistance among humans. But it has not been that easy.
"Over the past 30 years, we have learned that this hope was unrealistic as we share both pathogenic and benign bacteria with other humans and animals," said Summers, "and moreover bacteria transfer genes among themselves.
At the heart of the multi-resistance problem is integrons, which scientists have exclusively studied in such pathogenic bacteria as Salmonella and E. coli up to now. The UGA team wondered, however: Does the poultry production environment also harbor integrons that assemble these large clusters of distinct resistance genes?
To search for the answer, 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 the bacteria found 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. "Another intriguing point to note is that integrons and resistance genes were abundant regardless of antibiotic use on the farms. This suggests 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, not much 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 sketchy presently. However, since humans and their pets are "colonized" by similar bacteria, it would be reasonable to think that our companion animals and us also harbor such multi-resistance gene clusters which are enriched when we consume antibiotic or use it to treat our pets.
Humans and animals have billions of bacteria in and on their bodies at any time. 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 the treatment options are limited, if bacteria in the same environment are already equipped with clusters of genes conferring resistance to many antibiotics and could readily exchange these clusters.
"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.
For Summers and her colleagues in microbiology and the College of Veterinary Medicine at UGA, the discovery now allows them 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 which areas will develop resistance to new antibiotics. In addition, it will show us how fast and how far it will spread, and the implications for all antibiotic use, which are not merely restricted to 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 provided free access to their facilities for sample collection.