Abstract
The bacterium Escherichia coli 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 E. coli can colonize such niches and become pathogenic. We used experimental evolution to determine the speed and evolutionary paths undertaken by a commensal strain of E. coli 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 rfaI, fhuA and tppB, 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 E. coli into intracellular pathogens are dominated by a few pathoadaptive mutations with very strong effects.
Highlights
Bacterial populations have an enormous potential to adapt to their environments
A more complex pattern may emerge if adaptive mutations are very common and cause clonal interference [15], which may slow the loss of neutral variation [13], or if coexisting interdependent ecotypes emerge [16,40]
In our experimental evolution protocol, MFs (105/ml) were infected with E. coli for 24 hours, after which all extracellular bacteria were killed with gentamicin. 104 bacteria sampled from the intracellular environment of MFs were used to infect new uninfected MFs
Summary
Bacterial populations have an enormous potential to adapt to their environments. This is inferred from studies of molecular evolution and variation that find signatures of selection in many genes [1,2]. The remarkable pace of bacterial adaptation can be directly demonstrated in the laboratory by following evolution in real time, over many generations, in controlled environments with specific selection pressures [3,4,5]. Many studies of microbial evolution in real time involve studying adaptation to simple abiotic environments consisting of single or multiple sugars [6,7], characterizing compensation to the costs of deleterious mutations, such as antibiotic resistance genes in drug free environments [8,9], or studying adaptation in spatially structured environments [10,11,12]. The vast majority of these experiments demonstrate the acquisition of adaptive mutations at high rates, PLOS ONE | DOI:10.1371/journal.pone.0146123 January 11, 2016
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