Escherichia coli was isolated from biopsies taken from different regions of the lower gastro-intestinal tract of 61 humans living in the Canberra region. Up to 20 isolates were characterised from each gut region sampled using a REP-PCR fingerprinting approach and assigned to one of the eight E. coli phylogroups.
From 1-11 genotypes, average 3.6, were recovered per patient. The average number of strains per gut region was lowest in the terminal ileum, ascending and descending colon and highest in the transverse colon and rectum. The distribution of E. coli genotypes among gut regions was significantly non-random in 58% of the patients hosting more than a single strain. The extent to which strains were non-randomly distributed among gut regions depended on the phylogroup membership of the numerically dominant strain. Overall, there was less among gut region heterogeneity when the patient’s dominant strain belonged to phylogroup B2. Although strains were significantly non-randomly distributed among gut regions, phylogroups were not. When a host harboured two or more strains of E. coli, the phylogroup membership of the second most numerically dominant strain was significantly more likely to be a member of the same phylogroup as the dominant strain. The distribution of particular genotypes also indicates that some strains of E. coli may exhibit site-specificity, particularly with respect to the terminal ileum and rectum.
The results of this study provide additional evidence that E. coli strain diversity within a host is driven by among strain competition, as well as gastro-intestinal dynamics. Further the results of the study also demonstrate that the environment of the host’s lower gastro-intestinal tract, in part, determines the phylogroup membership of the strains in a host. Although gut site specificity has been reported for some E. coli diarrhoeal pathogens, the results of this study also indicate that some commensal strains may also exhibit site-specificity.