Within-host evolution and immigration of Escherichia coli in the human gastrointestinal tract

Abstract

Several studies have shown that when a human host harbours two or more strains of E. coli, the second strain is significantly more likely to be a member of the same phylogroup than to be a member of a different phylogroup. Such an outcome may be the consequence of a within host evolution event or due an independent immigration/establishment event. To determine the relative importance of these two types of events in determining E. coli diversity in a host, a large collection of E. coli that consisted of up to 100 isolates recovered from each of 69 patients undergoing colonoscopies was used. Whole genome sequence data was available for 174 isolates selected to represent one example of every REP-fingerprint type identified in a patient. Sequence type characterisation and single-nucleotide polymorphism analysis revealed that 83% of the strains observed in the host population were a consequence of immigration/establishment events. Restricting the analysis to those hosts harbouring two or strains belonging to the same phylogroup revealed that in about half of these cases the presence of a second strain belonging to the same phylogroup was the consequence of an independent immigration/establishment event. Single nucleotide polymorphism analysis coupled with the assumption of a mutation rate of 1.1 nucleotides/year indicated a residence time for those strains inferred to have evolved within the host of 1.2 years and a maximum estimated residence time of 11 years. This study has shown that when a host harbours two strains of the same phylogroup, then in about half of such cases, this is due to the immigration and establishment of strains and not within host evolution. Thus, the results of this study show that despite hosts being regularly exposed to a diversity of E. coli through the food that they eat, factors related to the host, at least in part, determines what E. coli strains succeed in establishing.