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The origins of antibiotic resistance

By comparing thousands of bacterial genomes, researchers have traced back the evolutionary history of antibiotic resistance genes.

Antibiotic resistance

Antibiotic resistance has become a major threat to modern medicine. Resistance genes to almost all classes of antibiotics have emerged. Mobile antibiotic resistance genes (ARGs) are associated with a variety of mobile genetic elements (MGEs). As a result, this has enabled these genes to spread to new hosts. The use and overuse of antibiotics has provided an advantage to those bacteria that have acquired resistance gene. This has promoted further spread of resistance and made it more difficult to treat infections.

Over the last decade, advances in DNA sequencing have made it possible to study bacterial evolution more effectively. Understanding which bacterial taxa these resistance genes mobilised from, and whether their origin taxa share common traits, is important for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge could aid in our ability to limit or delay further transfer of novel resistance genes.

Identifying origins

In a study, published in Communications Biology, researchers established a set of comparative criteria that can be used to identify the origins of mobile ARGs. Specifically, the team explored the scientific literature for claims of recent origins for antibiotic resistance genes. They combined this information with information from public DNA sequence databases and scrutinised the evidence at hand.

Researchers often speculate that antibiotic-producing bacteria are the source for antibiotic resistance gene. However, in this study the team found that none of the origin species were known antibiotic producers. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals. It appears that the clinical emergence of these resistance is a consequence of antibiotic selection pressure on taxa that are associated with the human/domestic animal microbiome.


Knowing where resistance genes originate from can help inform measures to delay emergence of additional resistance genes in the clinic. However, the authors noted that the origin for more than 95% of all known resistance genes is still unknown.

Professor Joakim Larsson, senior author, stated:

“Most likely, most of them come from un-sequenced bacterial species. We know the majority of the species that frequently tend to reside in the gut or on the skin of ourselves and of domestic animals. Therefore, this points to an important role of a much less explored gene reservoir – the environmental microbiota. The role of the environment as a likely source for antibiotic resistance also stress the need reduce risks for resistance development in the environment, for example by limiting discharges of antibiotics though wastewaters.”

Image credit: By macrovector –

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