Drought Leads to Increased Antibiotic-Resistant Microbes in Soils

A new Caltech study indicates that drought increases the abundances of antibiotic-resistant microorganisms in soils, which directly correlates with an increase in antibiotic-resistant infections in hospitals. In other words, regions experiencing high aridity—hotter, drier regions—also experience higher levels of antibiotic-resistant infections. The work demonstrates the interconnectedness of climate, environment, and human health.

The study was led by Caltech postdoctoral scholar Xiaoyu Shan and conducted in the laboratory of Dianne Newman, the Gordon M. Binder/Amgen Professor of Biology and Geobiology. A paper describing the research appears in Nature Microbiology on March 23.

Droughts are increasing in frequency and duration around the world due to climate change. Many studies have examined how microbes are able to tolerate the stress of aridity, but, until now, researchers hadn't examined what happens to the natural antibiotics in the soil during dry periods.

Microorganisms in soil naturally produce compounds that help them defend themselves against other competing microbes (among other functions). These natural compounds have been used by synthetic chemists as the scaffolds on which to build modern clinical antibiotics, and soil is a natural reservoir in which to discover new antibiotic candidates. However, in the same way that infectious pathogens can evolve resistance to clinical antibiotics, bacterial species in soils can do the same, leading to ever-evolving competition.

For the new study, Shan built a computational program to examine public datasets of microbial sequences in soil samples from all over the world, looking for the genes that enable the production of diverse antibiotics. He and his collaborators found that microbes producing antibiotic compounds are more abundant in drier soils. They hypothesize that, as soil dries, the available living space for microbes shrinks in volume, leading to more and more bacteria coming into contact with antibiotic compounds, killing them off, and leading to an enrichment in certain bacteria. The microbes that survive in this environment are those with a better ability to resist antibiotic compounds, which includes antibiotic producers but also other strains that harbor resistance genes.

The team then aimed to determine if more antibiotic-resistant microbes in the soil might correlate with more antibiotic-resistant infections in hospital settings in those regions. Examining datasets tracking antibiotic-resistant infections in hospitals that compared that data with geographical information on aridity, they found a strong correlation between higher incidences of antibiotic-resistant infections in hospitals and higher aridity, indicating that selection for antibiotic resistance in soils by drought can impact human populations.

"We're interacting with soil all the time, whether it's recreational or simply by inhaling dust," Shan says. "Importantly, bacteria are able to transfer genes to each other, and antibiotic-resistance genes are known to have a high rate of transfer. With trillions of bacteria in the environment, this is a substantial occurrence."

Newman emphasizes that this work is an example of how climate, environment, and human health are all linked. "Droughts are creating the same effects as overuse of antibiotics in the clinic: They both drive selection for antibiotics resistance," she explains. "The striking correlation Xiaoyu discovered motivates the development of better, faster diagnostics in clinical settings, as well as the development of novel therapeutic approaches."

The team next plans to use AI tools to discover and understand the mechanisms that bacteria utilize to resist and modify antibiotics.

The paper is titled "Drought drives elevated antibiotic resistance across soils." In addition to Shan and Newman, Caltech co-authors are undergraduate Karen Cao; postdoctoral scholars Hannah Jeckel, Reinaldo E. Alcalde, and Inês B. Trinidade; and graduate student Jarek V. Kwiecinski (MS '23). Funding was provided by the Doren Family Foundation, the Resnick Sustainability Institute at Caltech, the Division of Biology and Biological Engineering Nemko Postdoctoral Fellowship at Caltech, a Helen Hay Whitney Postdoctoral Fellowship, the National Science Foundation, and an EMBO Postdoctoral Fellowship.