Title: Following evolution after the horizontal transfer of synonymous versions of an antibiotic resistance gene.

Abstract: Horizontal gene transfer is a powerful mechanism by which antibiotic resistance spread among species. Despite this evolutionary success, there are a number of obstacles and mechanistic costs to the physical transfer and the maintenance of horizontally transferred genes. Here, I will focus on one of these mechanisms: transferred genes usually have codon preferences that differ from the ones of the receiving genome. This leads to translation errors, low translation rates and finally to low activity of the transferred gene and energetic costs for the receiving cell. It is thus predicted that (1) a gene with strong codon usage mismatch will generate a cost for the receiving cell and (2) its maintenance in the genome will trigger evolutionary changes both within and outside the transferred gene.

To test these predictions, three synonymous versions of the Chloramphenicol Acetyl Transferase with different codon preferences were transformed in Escherichia coli. We verified that the mismatch in codon usage induced a fitness cost. This cost was compensated during experimental evolution in presence of chloramphenicol and this compensation was associated to a diversity of genomic changes including changes in the regulation of the translation of the transferred gene, large duplications, mutators, point mutations in global regulators... Temporal analysis revealed the importance of clonal and plasmid interference in the post-HGT evolutionary dynamics. Finally, horizontal transfer of antibiotic resistance gene reveals itself, not only as a spreading highway for these genes but also as a powerful mechanism pushing bacteria to explore new ways of functioning.