Early settlers: which E. coli strains do you not want at birth?

The intestinal microbiota exerts vital biological processes throughout the human lifetime, and imbalances in its composition have been implicated in both health and disease status. Upon birth, the neonatal gut moves from a barely sterile to a massively colonized environment. The development of the intestinal microbiota during the first year of life is characterized by rapid and important changes in microbial composition, diversity, and magnitude. The pioneer bacteria colonizing the postnatal intestinal tract profoundly contribute to the establishment of the host-microbe symbiosis, which is essential for health throughout life. Escherichia coli is one of the first colonizers of the gut after birth. E. coli is a versatile population including harmless commensal, probiotic strains as well as frequently deadly pathogens. The prevalence of the specific phylogenetic B2 group, which encompasses both commensal and extra- or intraintestinal pathogenic E. coli strains, is increasing among E. coli strains colonizing infants quickly after birth. Fifty percent of the B2 group strains carry in their genome the pks gene cluster encoding the synthesis of a nonribosomal peptide-polyketide hybrid genotoxin named colibactin. In this review, we summarize both clinical and experimental evidence associating the recently emerging neonatal B2 E. coli population with several pathology and discuss how the expression of colibactin by both normal inhabitants of intestinal microflora and virulent strains may darken the borderline between commensalism and pathogenicity.