THE largest metagenomic search for antibiotic resistance genes in the DNA sequences of microbial communities from around the globe has found that bacteria carrying those genes turn up everywhere in nature.
The findings — reported in the May 8 edition of the journal Current Biology — add to the evidence showing just how common and abundant those resistance genes really are in natural environments.
This big-picture, ecological view on this growing health care concern emphasizes the important relationship between antibiotic resistance in the clinic and environmental microbiology, the researchers said.
"While the environment is known to harbor antibiotic-resistant strains of bacteria, as proven by many preceding studies, we did not really know the extent of their abundance," said Joseph Nesme of the Universite de Lyon in France. "The fact that we were able to detect antibiotic resistance genes at relatively important abundance in every environment tested is certainly our most striking result."
The researchers, including Nesme and senior author Pascal Simonet, took advantage of the ever-growing reams of existing next-generation sequencing data that are freely available in public repositories, along with information about antibiotic resistance genes found in pathogens infecting patients in clinics.
"Our strategy was simply to use all these pre-existing data and combine them to answer more precisely the question of antibiotic resistance prevalence in the environment," Nesme said.
The analyses detected antibiotic resistance gene determinants in all 71 environments represented in the public data, including soil, oceans and human feces. Samples collected from soil contained the most diverse pool of resistance genes, the researchers found. The most common types of resistance uncovered were efflux pumps and other genes conferring resistance to vancomycin, tetracycline or beta-lactam antibiotics, which are in common use in veterinary and human health care.
Despite all of this, Simonet said the researchers know that today's technologies are still unable to capture all of the diversity present in the environment.
There is a very good reason microbes would be armed with antibiotic resistance genes, the researchers explained. After all, most antibiotics used in medicine are isolated from soil microorganisms such as bacteria or fungi, which means that the resistance genes were available long before humans put antibiotic drugs into use. Bacteria lacking resistance genes to start with can simply borrow them (via horizontal transfer of genes) from those that do have them.
"It is only with more knowledge on antibiotic resistance dissemination — from the environment to pathogens in the clinic and leading to antibiotic treatment failure rates — that we will be able to produce more sustainable antibiotic drugs," Nesme said.