Lessons from twenty years of the life of commensalEscherichia colipopulations in a human gut

Abstract

Escherichia coliis an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210E. colinatural isolates from 22 stools sampled during a 20-year period in a healthy man (ED) living in France, who did not take any antibiotics. All the phylogroups, except the C, were represented with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty five clones were identified and classified in three phenotypes according to their abundance and persistence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four out of the five dominant/resident clones belonged to B2 phylogroup [sequence types (STs)131 and 452] and F-ST59, whereas sub-dominant/transient clones belonged mainly to numerous distinct B1, A and D phylogroup STs. The long residence time of B2 phylogroup clones was counterbalanced by lower colonization ability. Residence time and within-host frequency were positively correlated. By comparing ED strain genomes to a collection of commensalE. coligenomes from 359 French individuals, enriched/specific ED strain genome traits were identified including a metabolic pathway (mhpcluster) and a very rarely reported antiviral defense island encompassing dGTPase and/or Detocs systems. SNP analysis of clonal diversity showed neutral evolution. The normalE. coligut microbiota is shaped by both the intrinsic properties of the strain lineages and the environmental constraints.