Antibiotic resistance genes are essentially everywhere

The largest search for antibiotic resistance genes from around the globe has found that bacteria carrying those genes turn up everywhere in nature.

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 that scientists look for them. The findings reported in the Cell Press journal Current Biology on May 8 add to evidence showing just how common and abundant those resistance genes really are in natural environments.

This big-picture, ecological view on a growing healthcare 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 of the study Pascal Simonet, took advantage of the ever-growing reams of existing next-generation sequencing data that are freely available in public repositories together with information about antibiotic resistance genes found in pathogens infecting patients in the clinic.

"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 scientists' 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 healthcare.

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