New genes give gut bacteria antibiotic resistance

Study also finds that the same genes can lead to resistance when inserted into E. coli

The human gut is a reservoir of antibiotic resistance. And the bacteria residing there could bequeath their gift of resistance  to more harmful microbes under the right conditions, researchers report in the August 28 Science.

GENE EXCHANGE This illustration depicts a hypothetical situation in which disease-causing bacteria (with spiky green coats) could acquire resistance to the antibiotic penicillin by exchanging DNA (red helical ribbon) with harmless bacteria living in the human gut (blue rounded chains). Penicillin (white and green balls) would have no effect on microbes with the penicillin resistance gene (spiky blue coat). Courtesy of A. Canossa, M. Sommer and G. Dantas

Researchers at Harvard Medical School have found more resistance genes in indigenous gut bacteria than were known to exist. So far, the team has identified more than a hundred new genes conferring resistance to up to 13 antibiotics. All of these genes retain that role when inserted into E. coli bacteria, the authors say.

“This is the tip of the iceberg of what we will find when we start looking at all the bacteria in our gut that we mainly just ignore,” says infectious disease physician Vincent Young of the University of Michigan in Ann Arbor.

While some bacteria in the gut help people digest food, many are considered harmless freeloaders that have “found a good seat at the table,” Young says. But just as pathogens, including methicillin-resistant Staphylococcus aureus, are developing immunities to antibiotics, the mostly harmless bacteria in the gut may be developing resistances as well.

The researchers tested bacteria from the feces and saliva of two people for genes that would allow the bacteria to grow in environments with one of 13 common antibiotics.

“I think it’s a very good study,” says molecular biologist and microbiologist Stuart Levy of Tufts University in Boston. However, he says, people should not assume that this resistance is an effect of antibiotic use. It could just be a more general, natural reaction to the food and other substances that gut bacteria encounter every day.

Previous tests of antibiotic resistance in human gut bacteria have looked only at bacteria that grow well in a laboratory. But the Harvard group used a recently developed method to insert DNA from bacteria that are difficult to grow in the lab directly into more easily grown bacteria. In DNA from both lab-friendly and lab-loathing bacteria, the team has found 215 genes conferring antibiotic resistance so far. More than a hundred of these genes had never been identified before.

Though some bacteria are known to transfer genes among themselves, scientists have not yet found evidence that harmless bacteria in the gut have passed antibiotic resistance to pathogens.
If bacteria can exchange the newly found genes, then the fact that E. coli can use the genes suggests to coauthor Morten Sommer of Harvard Medical School that the resistance would also be transferred. However, even if this gene transfer could occur, it’s not clear how often it would happen, he says.

“Given that there are billions of people out there, and lots of pathogens, even rare events do happen,” Sommer says.

The team also found that a small subset of bacteria in the human gut harbored resistance genes that are identical to genes found in pathogens, which Sommer and his colleagues report indicates a past relationship.

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