Abstract
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.
Highlights
Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics
We show that all confirmed origin taxa are Proteobacteria, several species being the origin of several antibiotic resistance genes (ARGs) and almost all associated with infection in humans or domestic animals
But commonly not associated with the mobile genetic elements (MGEs)(s) (e.g., Insertion sequences (ISs), integron, transposon, plasmid, or as part of an integron) that played a role in the ARGs transition to its clinically relevant contexts
Summary
Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. 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 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. The lack of known origins for the great majority of ARGs points towards unsequenced environmental bacteria as likely sources
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