The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.

Programme Hospitalier Recherche Clinique, Institut Pasteur, Inserm, French Public Health Agency.

Host genetic factors appeared to be the predominant determinant for S. aureus persistent nasal carriage in humans.

Though microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin resistant strain 536, in the digestive tract of streptomycin treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on Dgalactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the non-random associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that "evolve and sequence" approach coupled to an analysis of Data accessibilityThe date used to produce the figure 1, 4, 5 and 6 are accessible on the Dryad website : (http://datadryad.org) with the number doi: 10.5061/dryad.4g503 and in the table S1The date used to produce the figures 2 and 3 are presented in the convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.

and evolution experiments on revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10 per base per year of the chromosome for ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (N ≈ 500 - 1700). In this study we follow the genomic fate of a dominant clone of in the human gut of a healthy individual over about a year. We could compute a low annual mutation rate that supports a low diversity and we could not retrieve any clear signature of selection. These observations support a neutral evolution of in the human gut, compatible with a very limited effective population size that deviates drastically with the observations made previously in experimental evolution.

We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an isolated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated and 198 wild animals were collected in the close proximity of the village. The prevalence of E. coli was decreasing from humans (100%) to human associated (64%) and wild (45%) animals. A clear genetic structure between these three E. coli populations was observed with human strains belonging very rarely to B2 phylogroup (3.7%), exhibiting few virulence genes and bacteriocins but being antibiotic resistant whereas wild animal strains were characterized by 46.1% of B2 phylogroup belonging, with very unique and infrequent sequence types, numerous extraintestinal genes and bacteriocins but no antibiotic resistance; the human-associated animal strains being intermediate. Furthermore, an unexpected genetic diversity was observed among the strains, as the housekeeping gene nucleotide diversity per site of the Trois-Sauts's strains was higher than the one of reference strains representative of the known species diversity. The existence of such E. coli structured phylogenetic diversity within various hosts of a single localization has never been reported.

SummaryEscherichia coli is a widespread commensal of the vertebrate intestinal tract. Until recently, no strong association between a particular clone and a given host species has been found. However, members of the B2 subgroup VIII clone with an O81 serotype appear to be human host specific. To determine the degree of host specificity exhibited by this clone, a PCR-based assay was used to screen 723 faecal and clinical isolates from humans, and 904 faecal isolates from animals. This clone was not detected among the animal isolates, but was discovered in people living in Africa, Europe and South America. The clone is rarely isolated from people suffering from intestinal or extraintestinal disease and is avirulent in a mouse model of extraintestinal infection. Fine-scale epidemiological analysis suggests that this clone is competitively dominant relative to other members of the B2 phylogenetic group and that it has increased in frequency over the past 20 years. This clone appears to be a good candidate for use as a probiotic, and may be suitable as an indicator of human faecal contamination in microbial source tracking studies.

BI mostly occurs as a first complication and represents a turning point in the course of compensated viral cirrhosis. Its occurrence impacts long-term prognosis and may define a subgroup of patients in whom adaptation of management is warranted.