Gut microbiota could inhibit the growth of antibiotic-resistant bacteria

A new study shows that interactions with the resident gut microbiota could suppress the proliferation and antibiotic-resistance evolution of superbugs.
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• Microbiota effects
• Antibiotic-resistance genes
• Bacterial interactions

What is already known on this topic
Around the world, overuse of antibiotics is driving the spread of bacterial “superbugs” that are resistant to antimicrobials, making people more vulnerable to diseases like tuberculosis and bacterial pneumonia. To counter the spread of antibiotic-resistant bacteria, it is important to understand how resistance spreads within microbial communities.

What this research adds
Researchers looked at the effect of three human gut microbiota communities on the growth and resistance evolution of a strain of Escherichia coli. Gut microbial communities suppressed E. coli growth and gut colonization, and prevented it from evolving antibiotic resistance. The E. coli strain only evolved antibiotic resistance in the absence of the gut microbiota.

Conclusion
The findings support the idea that interactions with resident microbiota can inhibit antibiotic-resistance evolution of bacterial species.

Around the world, overuse of antibiotics is driving the spread of bacterial “superbugs” that are resistant to antimicrobials, making people more vulnerable to diseases like tuberculosis and bacterial pneumonia. A new study shows that interactions with the resident gut microbiota could suppress the proliferation and antibiotic-resistance evolution of superbugs.

The findings, published in PLOS Biology, could help to predict resistance evolution from genetic data collected through surveillance efforts, the study authors say.

To counter the spread of antibiotic-resistant microbes, scientists have been looking at how resistance is acquired by bacteria and how it spreads within microbial communities. Interactions with other microbial communities might reduce the proliferation of superbugs through competition for resources or space. On the other hand, these relationships may also stimulate the growth and evolution of resistant bacteria through the exchange of genetic material.

To analyze the impact of interactions with other microorganisms on antibiotic-resistance evolution, Michael Baumgartner at ETH Zürich in Switzerland and his colleagues grew a strain of Escherichia coli in the presence or absence of an antibiotic and of three samples of gut microbiota, each from a different person.

Microbiota effects

In the presence of the antibiotic and the gut microbiota samples, the E. coli strain became less abundant or completely disappeared. In the absence of the antibiotic, microbiota communities still suppressed the E. coli strain on average, but the effect varied depending on the sample origin. The microbiota from human donor 3 suppressed the growth of the E. coli strain by about 54%, while the microbiota from donor 2 reduced the proliferation of E. coli by 24%. The microbiota from donor 1 completely eliminated the E. coli strain.

At the beginning of the experiment, all the microbiota communities were dominated by Lachnospiraceae and Ruminococcaceae. However, these bacteria became less abundant over time.

Antibiotic-resistance genes

The researchers did not observe resistant variants of the E. coli strain when they exposed it to the microbial communities from human microbiota samples. But resistant variants appeared towards the end of the experiment in the absence of the gut microbiota communities. “Thus, the resident microbial community from human microbiome samples suppressed antibiotic-resistance evolution in our [E. coli] strain,” the researchers say.

When the team analyzed the DNA of the antibiotic-resistant strains, they found mutations in genes related to membranes, stress responses, and transcription. Some of these genes are known to be involved in resistance to a specific class of antibiotics.

Bacterial interactions

Further experiments showed that specific conditions in the gut microbiota communities from human donors influenced the bacteria’s ability to transfer antibiotic-resistance genes. The findings, the researchers say, “can explain why our [E. coli] strain failed to acquire some of these beneficial resistance genes.”

The findings support the idea that interactions with resident microbiota can inhibit antibiotic-resistance evolution of bacterial species. However, more work in needed to uncover specific bacterial families within the gut microbiota that affect colonization and antibiotic-resistance evolution of invading species, the researchers say. Identifying resistance genes and acquiring information about factors that influence the genetic transfer of such genes will be important to combat the spread of superbugs, they say.