Soil microbe secrets could help halt superbugs

"We suspect that one of the primary factors that drives the sharing of antibiotic resistance genes is exposure to new antibiotics," says Gautam Dantas. "Because soil bacteria need many thousands of years to develop new antibiotics, the bacteria in that community don't encounter these threats anywhere near as often as disease-causing bacteria, which we regularly treat with different antibiotics." (Credit: Ian Sane/Flickr)

Microbes in soil may help identify ways to reduce gene-sharing among infectious bacteria, which could slow the spread of drug-resistant superbugs.

Drug-resistant bacteria annually sicken 2 million Americans and kill at least 23,000. A driving force behind this growing public health threat is the ability of bacteria to share genes that provide antibiotic resistance.

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Bacteria that naturally live in the soil have a vast collection of genes to fight off antibiotics, but they are much less likely to share these genes. The findings suggest that most genes from soil bacteria are not poised to contribute to antibiotic resistance in infectious bacteria.

“Soil bacteria have strategies for fighting antibiotics that we’re only just starting to learn about,” says Gautam Dantas, assistant professor of pathology and immunology at Washington University in St. Louis. “We need to make sure the genes that make these strategies possible aren’t shared with infectious bacteria, because they could make the problem of drug-resistant infections much worse.”

Most of the antibiotics used to fight illness today were devised by soil microbes, which employ them as weapons in the competition for resources and survival. Penicillin, the first successful antibiotic, came from the soil fungus Penicillium.

But widespread use of penicillin and other newer antibiotics has prompted bacteria to evolve strategies for blocking, evading, or otherwise resisting these drugs. Antibiotic-resistant disease now adds $20 billion to annual health-care costs and leads to 8 million additional hospital treatment days in the United States.

3,000 antibiotic resistance genes

For the new study, published in the journal Nature, the scientists analyzed bacterial DNA in 18 soil samples from agricultural and grassland sites from Minnesota and Michigan. They isolated small fragments of bacterial DNA from the soils and screened those pieces for genes that confer antibiotic resistance.

Other scientists have identified sections of genetic code that make it possible for bacteria to share genes. A gene must be close to these “mobility elements” to be shared. The approximately 3,000 antibiotic resistance genes the researchers identified in soil bacteria typically were not close to such elements.

Antibiotic-resistance genes in soil are linked tightly to specific bacteria, suggesting little sharing between species. In infectious bacteria, though, more frequent sharing of genes creates antibiotic-resistance portfolios that differ greatly among related bacteria.

“We suspect that one of the primary factors that drives the sharing of antibiotic resistance genes is exposure to new antibiotics,” Dantas says. “Because soil bacteria need many thousands of years to develop new antibiotics, the bacteria in that community don’t encounter these threats anywhere near as often as disease-causing bacteria, which we regularly treat with different antibiotics.”

Dantas and his colleagues continue to study factors that affect the spread of drug resistance in bacterial communities in hospitals, the environment, and the human digestive tract.

“We were happy to find that antibiotic resistance genes from soil bacteria generally aren’t poised to jump suddenly into pathogens,” Dantas says. “But we want to do everything we can—whether it’s changing how we treat infections in medical clinics or altering the way we manage the environments where bacteria grow—to keep the odds stacked against sharing of these genes.”

The Children’s Discovery Institute, the International Center for Advanced Renewable Energy and Sustainability at Washington University, the National Academies Keck Futures Initiatives, and the National Institutes of Health funded the study.

Source: Washington University in St. Louis