Escherichia coli Genomic Diversity within Extraintestinal Acute Infections Argues for Adaptive Evolution at Play

Abstract

Adaptive processes in chronic bacterial infections are well described, but much less is known about the processes at play during acute infections. Here, by sequencing seven randomly selected isolates per patient, we analyzed Escherichia coli populations from three acute extraintestinal infections in adults (meningitis, pyelonephritis, and peritonitis), in which a high-mutation-rate isolate or mutator isolate was found. The isolates of single patients displayed between a few dozen and more than 200 independent mutations, with up to half being specific to the mutator isolate. Multiple signs of positive selection were evidenced: a high ratio of nonsynonymous to synonymous mutations (K_a /K_s ratio) and strong mutational convergence within and between patients, some of them at loci well known for their adaptive potential, such as rpoS, rbsR, fimH, and fliC For all patients, the mutator isolate was likely due to a large deletion of a methyl-directed mismatch repair gene, and in two instances, the deletion extended to genes involved in some genetic convergence, suggesting potential coselection. Intrinsic extraintestinal virulence assessed in a mouse model of sepsis showed variable patterns of virulence ranging from non-mouse killer to mouse killer for the isolates from single patients. However, genomic signature and gene inactivation experiments did not establish a link between a single gene and the capacity to kill mice, highlighting the complex and multifactorial nature of the virulence. Altogether, these data indicate that E. coli isolates are adapting under strong selective pressure when colonizing an extraintestinal site.IMPORTANCE Little is known about the dynamics of adaptation in acute bacterial infections. By sequencing multiple isolates from monoclonal extraintestinal Escherichia coli infections in several patients, we were able to uncover traces of selection taking place at short time scales compared to chronic infection. High genomic diversity was observed in the patient isolates, with an excess of nonsynonymous mutations, and the comparison within and between different infections showed patterns of convergence at the gene level, both constituting strong signs of adaptation. The genes targeted were coding mostly for proteins involved in global regulation, metabolism, and adhesion/motility. Moreover, virulence assessed in a mouse model of sepsis was variable among the isolates of single patients, but this difference was left unexplained at the molecular level. This work gives us clues about the E. coli lifestyle transition between commensalism and pathogenicity.

Keywords: Escherichia coli; bacteria; evolution; genomes; infection.

FIG 1

Mutation rates of the E. coli isolates from the three patients. The y axis represents the frequency of rifampicin resistance acquisition expressed as the median of at least nine values corresponding to three independent cultures. E. coli M13 and K-12 MG1655 are mutator (mutS-deleted) and nonmutator controls, respectively, and are shaded in gray. * indicates a mutator.

FIG 2

Unrooted trees of isolates from the three patients and molecular mechanism of the mutator genotype. The trees were constructed with the mutation presence/absence matrix using neighbor joining. Below each tree is a representation of the genomic deletion event giving a mutator phenotype, and the convergent mutations observed for some isolates are represented by colored diamonds. The scale bars below the trees are the numbers of substitutions. * indicates a mutator. DEL, deletion; INS, small insertion; SNP, single nucleotide polymorphism.

FIG 3

Mouse survival curves after infection by isolates from patients 13 and 17. All surviving mice were sacrificed after 164 h. * indicates a mutator.