Antibiotic resistance is a major public health crisis worldwide as bacteria develop the ability to defend themselves against many, sometimes all, of the antibiotics we have at our disposal. Infections caused by these bacteria are often life-threatening. In order to continue fighting these infections, we have to figure out how antibiotic resistance develops, evolves, and spreads.
Many people think that antibiotic resistance developed from the irresponsible use of antibiotics for illnesses like colds or the flu (antibiotics can not cure a viral infection), and that’s not wrong. We do have a huge part to play in the rise of the “superbug,” another name for antibiotic-resistant bacteria, but human antibiotic use is not the reason bacteria started becoming resistant to antibiotics.
It turns out they always have been.
Many microorganisms have been producing antibiotics for millions (potentially billions) of years. Antibiotics serve many purposes in nature and where there are antibiotics, there is antibiotic resistance.
All of the drugs we have currently are either natural products or derived from natural products, meaning that the genes encoding resistance to these drugs probably already exist somewhere. Bacteria can also mutate their genes when they are under stress in order to make new resistance genes that help them survive when antibiotics are present. Whether they already had a resistance gene or just developed it, they can share those genes with other bacteria in the population, through a process called horizontal gene transfer.
Knowing what resistance genes are already present in the environment is an important part of predicting how bacterial communities might react to the antibiotics we dump into the environment. This knowledge is crucial for planning out how to deal with infections and prevent outbreaks.
One of the best ways to figure out which antibiotic resistance genes are present in an environment that has not been influenced by humans is to study one, which is exactly what a group of researchers at the University of Pretoria, South Africa, did.
Researchers took soil samples from 17 sites in Antarctica that had no known exposure to human usage of antibiotics. They looked at the genes present in the samples using a process called “shotgun metagenomics,” in which DNA is extracted from environmental samples (in this case, from Antarctic soils). These bits of DNA are analyzed to reconstruct the genes carried by each species in the sample. For the first time in a pristine environment, the group used this method to describe the group of resistance genes, called the “resistome,” and identified the different bacteria present in each sample.
Across their 17 sites, researchers found 177 antibiotic resistance genes representing all of the known types of bacterial antibiotic resistance. They also found that the bacteria carrying the most resistance genes also carried genes for the production of the antibiotics they were resistant to, and these bacteria were found in less diverse populations. This means that bacteria could be actively using the production of antibiotics in the soil for a competitive advantage. The researchers also argue that the ancestral bacteria probably obtained their antibiotic resistance through horizontal gene transfer, but that the modern bacteria inherited it directly from their parent cells.
These findings are important because antibiotics end up in the environment through our trash, our agriculture, and our wastewater. This generates new genes and stimulates the transfer of old and new genes within microbial communities. Gene sharing produces an environmental “resistome,” a collection of resistance genes that many bacteria can use. Studying this resistome could help scientists inform doctors of what to expect in the clinic and help policy makers create effective strategies for combating infections caused by antibiotic-resistant bacteria.