Antimicrobial resistance in soil bacteria without the use of antibiotics

Overuse of antibiotics is currently the primary reason for the rise of antimicrobial resistance (AMR). Researchers at the Indian Institute of Science (IISc) and Kiel University, however, have shown that AMR can surprisingly be found in soil bacterial communities due to microbial interactions too, driven by a species of predatory bacteria.

Published in Current Biology, the study looked at how the presence of the bacterium Myxococcus xanthus affects the number of antimicrobial-resistant bacteria in soil samples. M. xanthus is a predatory species which is known to release antimicrobials and other molecules to kill its prey. The presence of this bacteria in soil microbial communities raises the question: Do other bacteria living with M. xanthus acquire resistance to these molecules over time?

“Human-driven [antibiotic] resistance is a major problem, but the question is: Are there other aspects that we completely ignore? This was very exciting [to explore],” says Samay Pande, Assistant Professor at the Department of Microbiology and Cell Biology (MCB), IISc, and corresponding author of the study.

Pande and others found that the death of M. xanthus in soil bacterial communities increased the frequency of resistant isolates – bacterial cells resistant to antibiotics – in many different species of soil bacteria. These cells also showed resistance to certain antibiotics even without exposure to these drugs.

When faced with starvation, populations of M. xanthus die en masse. In famine-like conditions, which are very common in soil environments, these bacterial cells form stress-resistant structures called fruiting bodies that are filled with spores. During the development of fruiting bodies, only a minority of cells succeed in becoming spores, whereas the majority of the bacterial cells undergo lysis (rupture) and release growth-inhibitory substances into the environment. The researchers believe that exposure to these growth inhibitory molecules is the reason behind the increased frequency of resistant isolates in the soil bacterial community. Interestingly, not all strains of M. xanthus triggered enrichment of resistance; it was the ones with higher diversity of biosynthetic clusters that seem to drive it.

When analysing these inhibitory molecules, the researchers found something even more interesting. “We identified multiple different molecules and did a very crude classification,” explains Saheli Saha, PhD student at MCB and co-first author of the study. “Individually, these molecules might not do anything, but when you put them together, they suddenly do this strange thing where they can enrich other resistant isolates.” The researchers found that resistance was enriched against several antibiotics, which include commonly used drugs such as tetracycline and rifampicin.

“It is important to test whether the observations derived from culturable bacteria are also applicable for unculturable microbes,” explains Jyotsna Kalathera, PhD student at MCB and one of the authors of the study. Therefore, the team also analysed the genomes of the bacterial communities in the soil. They found that AMR enriched through this phenomenon could be extended to unculturable bacterial species via similar exposure to growth inhibitory molecules.

The fact that AMR can be maintained by microbial antagonism even in the absence of human-driven contamination of antibiotics is a new and unexpected discovery, the researchers say. “We need to explore and find out if this is more common,” says Pande.

Understanding this phenomenon better might also help predict where such antibiotic-resistant bacteria live in nature, Saha suggests. “This is something that we have just tested with soil samples from India. Testing soil samples from different locations would help us understand more about this phenomenon.”