Trade-Offs of <i>Escherichia coli</i> Adaptation to an Intracellular Lifestyle in Macrophages

<div><p>The bacterium <i>Escherichia coli</i> exhibits remarkable genomic and phenotypic variation, with some pathogenic strains having evolved to survive and even replicate in the harsh intra-macrophage environment. The rate and effects of mutations that can cause pathoadaptation are key determinants of the pace at which <i>E</i>. <i>coli</i> can colonize such niches and become pathogenic. We used experimental evolution to determine the speed and evolutionary paths undertaken by a commensal strain of <i>E</i>. <i>coli</i> when adapting to intracellular life. We estimated the acquisition of pathoadaptive mutations at a rate of 10⁻⁶ per genome per generation, resulting in the fixation of more virulent strains in less than a hundred generations. Whole genome sequencing of independently evolved clones showed that the main targets of intracellular adaptation involved loss of function mutations in genes implicated in the assembly of the lipopolysaccharide core, iron metabolism and di- and tri-peptide transport, namely <i>rfaI</i>, <i>fhuA</i> and <i>tppB</i>, respectively. We found a substantial amount of antagonistic pleiotropy in evolved populations, as well as metabolic trade-offs, commonly found in intracellular bacteria with reduced genome sizes. Overall, the low levels of clonal interference detected indicate that the first steps of the transition of a commensal <i>E</i>. <i>coli</i> into intracellular pathogens are dominated by a few pathoadaptive mutations with very strong effects.</p>