A framework for identifying the recent origins of mobile antibiotic resistance genes

Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome. Ebmeyer and colleagues developed a genomic framework for identification and scrutiny of the origins of antibiotic resistance genes. Using data scoured from the literature and publicly available genomes, their results indicate that only 81% of previously reported origins are valid, and that the majority of resistance genes of which the origin is known to date emerged in taxa that have been associated with infection in humans and domesticated animals.

Automated summary

The emergence of antibiotic resistance genes is influenced by mobile resistance genes acquired through horizontal gene transfer. Majority of the resistance genes originated from taxa associated with infection in humans and domestic animals, likely due to antibiotic selection pressure.