title: Plasmid and clonal interference during post horizontal gene transfer evolution.
abstract: Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions. This conflict between cellular fitness and plasmid spread sets the scene for multilevel selection processes. We have engineered a system to study the short-term evolutionary impact of different synonymous versions of a plasmid-encoded antibiotic resistance gene. Applying experimental evolution under different selection conditions and deep sequencing allowed us to show rapid local adaptation to the presence of antibiotic and to the specific version of the resistance gene transferred. We describe the presence of clonal interference at two different levels: at the within-cell level, because a single cell can carry several plasmids, and at the between-cell level, because a bacterial population may contain several clones carrying different plasmids and displaying different fitness in the presence/absence of antibiotic. Understanding the within-cell and between-cell dynamics of plasmids after horizontal gene transfer is essential to unravel the dense network of mobile elements underlying the worldwide threat to public health of antibiotic resistance.
authors.affiliation: Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, 34293, Montpellier, France.|Laboratory MIVEGEC, UMR CNRS 5290, IRD 224, UM, Centre National de la Recherche Scientifique, 911 avenue Agropolis, BP64501, 34394, Montpellier Cedex 05, France.
authors.forename: S
authors.identifier: http://orcid.org/0000-0001-8075-0968
authors.initials: S
authors.lastname: Bedhomme
authors.affiliation: Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box 8940577, San Joaquín, Santiago, Chile.
authors.forename: D
authors.initials: D
authors.lastname: Perez Pantoja
authors.affiliation: Laboratory MIVEGEC, UMR CNRS 5290, IRD 224, UM, Centre National de la Recherche Scientifique, 911 avenue Agropolis, BP64501, 34394, Montpellier Cedex 05, France.
authors.forename: I G
authors.initials: IG
authors.lastname: Bravo
mesh_terms: D000222:Adaptation, Physiological; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D059014:High-Throughput Nucleotide Sequencing; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial
keywords: antibiotic resistance; clonal interference; codon usage preferences; multilevel selection; plasmid