Escherichia coli extra-intestinal population translocation in leukemia patients

Escherichia coli, a commensal species of the human gut, is an opportunistic pathogen which can colonize extra-intestinal compartments, including the bloodstream and the bladder, among others. Immunosuppressed patients are particularly prone to E. coli infections because of their porous intestinal barriers and the lack of immune defense. Here, we investigated whether these particular conditions could have modified the signature of selection in intra- and extra- intestinal compartments. In non-immunosuppressed patients, purifying (or neutral) evolution of E. coli populations is expected in the gut. Conversely, in extraintestinal compartments, E. coli genomes are under diversifying selection with strong evidence for adaptation. Moreover diverging adaptive mutations shape the allelic diversity of intestinal and bloodstream populations. Strikingly, investigating evolutionary forces in immunosuppressed patients, we found the same signature of selection in the gut and the bloodstream, as well as a limited number of non-specific mutations among compartments for non mutator isolates. In all cases, urine isolates were dominated by neutral selection. The weakening of the intestine wall and the compromised immune system leading to similar adaptive constraints among the gut and the bloodstream probably explain the observed homogeneity of E. coli strains isolated in those compartments.