Escherichia coli diversity in the lower intestinal tract of humans

Abstract

Previous studies examining the clonal diversity of Escherichia coli populations within humans have been based on faecal isolates. In this study E. coli were isolated from biopsies taken from the terminal ileum, ascending, transverse and descending colon, and rectum of 69 individuals. Multiple isolates from each biopsy were characterized using Rep-PCR. An average of 3.5 genotypes were recovered per host, and in hosts with two or more strains, the phylogroup membership of the second most abundant strain was significantly more likely to be the same as the dominant strain. There was no indication of a non-random distribution of E. coli phylogroups among the regions of the lower intestine. In hosts with multiple genotypes, as defined by Repetitive extragenic palindromic-PCR, genotypes were non-randomly distributed among gut regions in over half the individuals. The phylogroup membership of an individual's numerically dominant strain explained some of the variation in the extent to which strains within an individual were heterogeneously distributed, with most heterogeneity observed when the numerically dominant strain belonged to phylogroups E or F, and the least when the dominant strain belonged to phylogroup B2. The results of this study support previous studies on pigs that demonstrated faecal sampling underestimates the genotype diversity present within a host.

Comparative genomics of Crohn's disease-associated adherent-invasiveEscherichia coli

“…Strain ED1a was included because it was isolated from a healthy control, belongs to the B2 phylogroup and was found to be avirulent in a mouse lethality model 33. The 41 strains in this study were isolated from 36 Australian patients with and without IBD (14 CD; 5 UC; 21 non-IBD), as described in Gordon et al ;34 O'Brien et al ;7 and Gordon et al 35 Strain characteristics can be found in online supplementary material. All strains and tissues were stored at −80°C in luria broth (LB) glycerol until required.…”

“…Approximately 47% of strains isolated from human mucosal biopsies are phylogroup B2, which, when present in a host, are likely to be the dominant strain 19. The majority (64%) of AIEC isolates belong to the B2 phylogroup,12 and this phylogroup typically contains more virulence factors than strains belonging to other phylogroups 20.…”

“…Multilocus sequence typing (MLST) is also used to assign E. coli into sequence types (STs), using one of three schemes 21–23. Any mucosa-associated strain, regardless of phylogroup, is likely to be found along the length of the lower GI tract, and is unlikely to be restricted to a single region 19. ST95 strains are commonly isolated from humans and belong to the B2 phylogroup 24…”

The interplay ofEscherichia coliO157:H7 and commensalE. coli: the importance of strain-level identification

“…It was later suggested [18] that humans are colonized for long periods by E. coli termed 'resident', and by fleeting strains termed 'transient', indicating that strains humans carry are undergoing continuous turn-over. These early studies have been confirmed and extended by others [19], and more recently, Gordon et al studied 69 individuals and found that the number of E. coli strains varied from one to eight, and that there might be site specificity along the gastrointestinal tract [20].…”

Day-to-Day Dynamics of Commensal Escherichia coli in Zimbabwean Cows Evidence Temporal Fluctuations within a Host-Specific Population Structure

“…Nonetheless, it should be remembered that the diversity and distribution of the E. coli genotypes are different among the different regions of the gastrointestinal tract, as environmental conditions are not the same in each of these regions (45)(46)(47). Thus, we cannot exclude the possibility that the clones detected were present in different parts of the gastrointestinal tract of their host, and their prevalence at days 2, 15, and 25 could have been the result of a bloom of a specific clone in a given fraction of the gastrointestinal tract.…”